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Alsaad HN, Al-Jasani BM, Mahmood AAR, Tahtamouni LH, Saleh KM, AlSakhen MF, Kanaan SI, Yasin SR. Novel 1,3,4-oxadiazole derivatives of naproxen targeting EGFR: Synthesis, molecular docking studies, and cytotoxic evaluation. Drug Dev Res 2024; 85:e22231. [PMID: 38956926 DOI: 10.1002/ddr.22231] [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: 03/27/2024] [Revised: 05/24/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024]
Abstract
The close association between inflammation and cancer inspired the synthesis of a series of 1,3,4-oxadiazole derivatives (compounds H4-A-F) of 6-methoxynaphtalene. The chemical structures of the new compounds were validated utilizing Fourier-transform infrared, proton nuclear magnetic resonance, and carbon-13 nuclear magnetic resonance spectroscopic techniques and CHN analysis. Computer-aided drug design methods were used to predict the compounds biological target, ADMET properties, toxicity, and to evaluate the molecular similarities between the design compounds and erlotinib, a standard epidermal growth factor receptor (EGFR) inhibitor. The antiproliferative effects of the new compounds were evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay, cell cycle analysis, apoptosis detection by microscopy, quantitative reverse transcription-polymerase chain reaction, and immunoblotting, and EGFR enzyme inhibition assay. In silico analysis of the new oxadiazole derivatives indicated that these compounds target EGFR, and that compounds H4-A, H4-B, H4-C, and H4-E show similar molecular properties to erlotinib. Additionally, the results indicated that none of the synthesized compounds are carcinogenic, and that compounds H4-A, H4-C, and H4-F are nontoxic. Compound H4-A showed the best-fit score against EGFR pharmacophore model, however, the in vitro studies indicated that compound H4-C was the most cytotoxic. Compound H4-C caused cytotoxicity in HCT-116 colorectal cancer cells by inducing both apoptosis and necrosis. Furthermore, compounds H4-D, H4-C, and H4-B had potent inhibitory effect on EGFR tyrosine kinase that was comparable to erlotinib. The findings of this inquiry offer a basis for further investigation into the differences between the synthesized compounds and erlotinib. However, additional testing will be needed to assess all of these differences and to identify the most promising compound for further research.
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Affiliation(s)
- Hiba N Alsaad
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Basrah, Basrah, Iraq
| | - Baan M Al-Jasani
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Basrah, Basrah, Iraq
| | - Ammar A Razzak Mahmood
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Baghdad, Baghdad, Iraq
| | - Lubna H Tahtamouni
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Khaled M Saleh
- Department of Basic Dental Sciences, Faculty of Dentistry, The Hashemite University, Zarqa, Jordan
| | - Mai F AlSakhen
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Sana I Kanaan
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Salem R Yasin
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
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McCarthy KA, Marcotte DJ, Parelkar S, McKinnon CL, Trammell LE, Stangeland EL, Jetson RR. Discovery of Potent Isoindolinone Inhibitors that Target an Active Conformation of PARP1 Using DNA-Encoded Libraries. ChemMedChem 2024; 19:e202400093. [PMID: 38482564 DOI: 10.1002/cmdc.202400093] [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: 03/08/2024] [Indexed: 04/11/2024]
Abstract
Inhibition of poly (ADP-ribose) polymerase-1 (PARP1), a DNA repair enzyme, has proven to be a successful strategy for the treatment of various cancers. With the appropriate selection conditions and protein design, DNA-encoded library (DEL) technology provides a powerful avenue to identify small molecules with the desired mechanism of action towards a target of interest. However, DNA-binding proteins, such as PARP1, can be challenging targets for DEL screening due to non-specific protein-DNA interactions. To overcome this, we designed and screened a PARP1 catalytic domain construct without the autoinhibitory helical domain. This allowed us to interrogate an active, functionally-relevant form of the protein resulting in the discovery of novel isoindolinone PARP1 inhibitors with single-digit nanomolar potency. These inhibitors also demonstrated little to no PARP1-DNA trapping, a property that could be advantageous in the clinic.
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Affiliation(s)
- Kelly A McCarthy
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Douglas J Marcotte
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Sangram Parelkar
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Crystal L McKinnon
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Lindsay E Trammell
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Eric L Stangeland
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
| | - Rachael R Jetson
- Discovery Sciences, Valo Health, 75 Hayden Avenue, Lexington, MA, 02421, United States
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3
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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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4
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Velagapudi UK, Rouleau-Turcotte É, Billur R, Shao X, Patil M, Black BE, Pascal JM, Talele TT. Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks. Biochem J 2024; 481:437-460. [PMID: 38372302 PMCID: PMC11070930 DOI: 10.1042/bcj20230406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
Catalytic poly(ADP-ribose) production by PARP1 is allosterically activated through interaction with DNA breaks, and PARP inhibitor compounds have the potential to influence PARP1 allostery in addition to preventing catalytic activity. Using the benzimidazole-4-carboxamide pharmacophore present in the first generation PARP1 inhibitor veliparib, a series of 11 derivatives was designed, synthesized, and evaluated as allosteric PARP1 inhibitors, with the premise that bulky substituents would engage the regulatory helical domain (HD) and thereby promote PARP1 retention on DNA breaks. We found that core scaffold modifications could indeed increase PARP1 affinity for DNA; however, the bulk of the modification alone was insufficient to trigger PARP1 allosteric retention on DNA breaks. Rather, compounds eliciting PARP1 retention on DNA breaks were found to be rigidly held in a position that interferes with a specific region of the HD domain, a region that is not targeted by current clinical PARP inhibitors. Collectively, these compounds highlight a unique way to trigger PARP1 retention on DNA breaks and open a path to unveil the pharmacological benefits of such inhibitors with novel properties.
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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, USA
| | - Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal H3T 1J4 Canada
| | - Ramya Billur
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - Xuwei Shao
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, USA
| | - Manisha Patil
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, New York 11439, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - 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, USA
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Thakur A, Rana M, Ritika, Mathew J, Nepali S, Pan CH, Liou JP, Nepali K. Small molecule tractable PARP inhibitors: Scaffold construction approaches, mechanistic insights and structure activity relationship. Bioorg Chem 2023; 141:106893. [PMID: 37783100 DOI: 10.1016/j.bioorg.2023.106893] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
Diverse drug design strategies viz. molecular hybridization, substituent installation, scaffold hopping, isosteric replacement, high-throughput screening, induction and separation of chirality, structure modifications of phytoconstituents and use of structural templates have been exhaustively leveraged in the last decade to load the chemical toolbox of PARP inhibitors. Resultantly, numerous promising scaffolds have been pinpointed that in turn have led to the resuscitation of the credence to PARP inhibitors as cancer therapeutics. This review briefly presents the physiological functions of PARPs, the pharmacokinetics, and pharmacodynamics, and the interaction profiles of FDA-approved PARP inhibitors. Comprehensively covered is the section on the drug design strategies employed by drug discovery enthusiasts for furnishing PARP inhibitors. The impact of structural variations in the template of designed scaffolds on enzymatic and cellular activity (structure-activity relationship studies) has been discussed. The insights gained through the biological evaluation such as profiling of physicochemical properties andin vitroADME properties, PK assessments, and high-dose pharmacology are covered.
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Affiliation(s)
- Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Ritika
- College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Jacob Mathew
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Sanya Nepali
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
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Chen GQ, Guo HY, Quan ZS, Shen QK, Li X, Luan T. Natural Products-Pyrazine Hybrids: A Review of Developments in Medicinal Chemistry. Molecules 2023; 28:7440. [PMID: 37959859 PMCID: PMC10649211 DOI: 10.3390/molecules28217440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Pyrazine is a six-membered heterocyclic ring containing nitrogen, and many of its derivatives are biologically active compounds. References have been downloaded through Web of Science, PubMed, Science Direct, and SciFinder Scholar. The structure, biological activity, and mechanism of natural product derivatives containing pyrazine fragments reported from 2000 to September 2023 were reviewed. Publications reporting only the chemistry of pyrazine derivatives are beyond the scope of this review and have not been included. The results of research work show that pyrazine-modified natural product derivatives have a wide range of biological activities, including anti-inflammatory, anticancer, antibacterial, antiparasitic, and antioxidant activities. Many of these derivatives exhibit stronger pharmacodynamic activity and less toxicity than their parent compounds. This review has a certain reference value for the development of heterocyclic compounds, especially pyrazine natural product derivatives.
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Affiliation(s)
- Guo-Qing Chen
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China; (G.-Q.C.); (H.-Y.G.); (Z.-S.Q.); (Q.-K.S.)
| | - Hong-Yan Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China; (G.-Q.C.); (H.-Y.G.); (Z.-S.Q.); (Q.-K.S.)
| | - Zhe-Shan Quan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China; (G.-Q.C.); (H.-Y.G.); (Z.-S.Q.); (Q.-K.S.)
| | - Qing-Kun Shen
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China; (G.-Q.C.); (H.-Y.G.); (Z.-S.Q.); (Q.-K.S.)
| | - Xiaoting Li
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China; (G.-Q.C.); (H.-Y.G.); (Z.-S.Q.); (Q.-K.S.)
| | - Tian Luan
- Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
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Ramesh S, Almeida SD, Hammigi S, Radhakrishna GK, Sireesha G, Panneerselvam T, Vellingiri S, Kunjiappan S, Ammunje DN, Pavadai P. A Review of PARP-1 Inhibitors: Assessing Emerging Prospects and Tailoring Therapeutic Strategies. Drug Res (Stuttg) 2023; 73:491-505. [PMID: 37890514 DOI: 10.1055/a-2181-0813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Eukaryotic organisms contain an enzyme family called poly (ADP-ribose) polymerases (PARPs), which is responsible for the poly (ADP-ribosylation) of DNA-binding proteins. PARPs are members of the cell signaling enzyme class. PARP-1, the most common isoform of the PARP family, is responsible for more than 90% of the tasks carried out by the PARP family as a whole. A superfamily consisting of 18 PARPs has been found. In order to synthesize polymers of ADP-ribose (PAR) and nicotinamide, the DNA damage nick monitor PARP-1 requires NAD+ as a substrate. The capability of PARP-1 activation to boost the transcription of proinflammatory genes, its ability to deplete cellular energy pools, which leads to cell malfunction and necrosis, and its involvement as a component in the process of DNA repair are the three consequences of PARP-1 activation that are of particular significance in the process of developing new drugs. As a result, the pharmacological reduction of PARP-1 may result in an increase in the cytotoxicity toward cancer cells.
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Affiliation(s)
- Soundarya Ramesh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Shannon D Almeida
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Sameerana Hammigi
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Govardan Katta Radhakrishna
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Golla Sireesha
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Theivendren Panneerselvam
- Department of Pharmaceutical Chemistry, Swamy Vivekanandha College of Pharmacy, Elayampalayam, Tamil Nadu, India
| | - Shangavi Vellingiri
- Department of Pharmacy Practice, Swamy Vivekananda College of Pharmacy, Elayampalayam, Tamil Nadu, India
| | - Selvaraj Kunjiappan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Damodar Nayak Ammunje
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, India
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8
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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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9
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Montoya AL, Glavatskikh M, Halverson BJ, Yuen LH, Schüler H, Kireev D, Franzini RM. Combining pharmacophore models derived from DNA-encoded chemical libraries with structure-based exploration to predict Tankyrase 1 inhibitors. Eur J Med Chem 2023; 246:114980. [PMID: 36495630 PMCID: PMC9805525 DOI: 10.1016/j.ejmech.2022.114980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
DNA-encoded chemical libraries (DECLs) interrogate the interactions of a target of interest with vast numbers of molecules. DECLs hence provide abundant information about the chemical ligand space for therapeutic targets, and there is considerable interest in methods for exploiting DECL screening data to predict novel ligands. Here we introduce one such approach and demonstrate its feasibility using the cancer-related poly-(ADP-ribose)transferase tankyrase 1 (TNKS1) as a model target. First, DECL affinity selections resulted in structurally diverse TNKS1 inhibitors with high potency including compound 2 with an IC50 value of 0.8 nM. Additionally, TNKS1 hits from four DECLs were translated into pharmacophore models, which were exploited in combination with docking-based screening to identify TNKS1 ligand candidates in databases of commercially available compounds. This computational strategy afforded TNKS1 inhibitors that are outside the chemical space covered by the DECLs and yielded the drug-like lead compound 12 with an IC50 value of 22 nM. The study further provided insights in the reliability of screening data and the effect of library design on hit compounds. In particular, the study revealed that while in general DECL screening data are in good agreement with off-DNA ligand binding, unpredictable interactions of the DNA-attachment linker with the target protein contribute to the noise in the affinity selection data.
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Affiliation(s)
- Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Brayden J Halverson
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Lik Hang Yuen
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100, Lund, Sweden.
| | - Dmitri Kireev
- Department of Chemistry, 36 Schlundt Hall, University of Missouri, Columbia, MO, 65211, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, UT, 84112, USA.
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10
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Peng X, Pan W, Jiang F, Chen W, Qi Z, Peng W, Chen J. Selective PARP1 Inhibitors, PARP1-based Dual-Target Inhibitors, PROTAC PARP1 Degraders, and Prodrugs of PARP1 Inhibitors for Cancer Therapy. Pharmacol Res 2022; 186:106529. [DOI: 10.1016/j.phrs.2022.106529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
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11
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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: 13] [Impact Index Per Article: 6.5] [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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12
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Syam YM, Anwar MM, Abd El-Karim SS, Elokely KM, Abdelwahed SH. New Quinoxaline-Based Derivatives as PARP-1 Inhibitors: Design, Synthesis, Antiproliferative, and Computational Studies. Molecules 2022; 27:molecules27154924. [PMID: 35956876 PMCID: PMC9370283 DOI: 10.3390/molecules27154924] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/05/2022] Open
Abstract
Herein, 2,3-dioxo-1,2,3,4-tetrahydroquinoxaline was used as a bio-isosteric scaffold to the phthalazinone motif of the standard drug Olaparib to design and synthesize new derivatives of potential PARP-1 inhibitory activity using the 6-sulfonohydrazide analog 3 as the key intermediate. Although the new compounds represented the PARP-1 suppression impact of IC50 values in the nanomolar range, compounds 8a, 5 were the most promising suppressors, producing IC50 values of 2.31 and 3.05 nM compared to Olaparib with IC50 of 4.40 nM. Compounds 4, 10b, and 11b showed a mild decrease in the potency of the IC50 range of 6.35–8.73 nM. Furthermore, compounds 4, 5, 8a, 10b, and 11b were evaluated as in vitro antiproliferative agents against the mutant BRCA1 (MDA-MB-436, breast cancer) compared to Olaparib as a positive control. Compound 5 exhibited the most significant potency of IC50; 2.57 µM, whereas the IC50 value of Olaparib was 8.90 µM. In addition, the examined derivatives displayed a promising safety profile against the normal WI-38 cell line. Cell cycle, apoptosis, and autophagy analyses were carried out in the MDA-MB-436 cell line for compound 5, which exhibited cell growth arrest at the G2/M phase, in addition to induction of programmed apoptosis and an increase in the autophagic process. Molecular docking of the compounds 4, 5, 8a, 10b, and 11b into the active site of PARP-1 was carried out to determine their modes of interaction. In addition, an in silico ADMET study was performed. The results evidenced that compound 5 could serve as a new framework for discovering new potent anticancer agents targeting the PARP-1 enzyme.
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Affiliation(s)
- Yasmin M. Syam
- Department of Therapeutic Chemistry, National Research Center, Dokki, Cairo 12622, Egypt; (M.M.A.); (S.S.A.E.-K.)
- Correspondence: (Y.M.S.); (S.H.A.)
| | - Manal M. Anwar
- Department of Therapeutic Chemistry, National Research Center, Dokki, Cairo 12622, Egypt; (M.M.A.); (S.S.A.E.-K.)
| | - Somaia S. Abd El-Karim
- Department of Therapeutic Chemistry, National Research Center, Dokki, Cairo 12622, Egypt; (M.M.A.); (S.S.A.E.-K.)
| | - Khaled M. Elokely
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
| | - Sameh H. Abdelwahed
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, USA
- Correspondence: (Y.M.S.); (S.H.A.)
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13
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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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14
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Othman EM, Fayed EA, Husseiny EM, Abulkhair HS. Apoptosis induction, PARP-1 inhibition, and cell cycle analysis of leukemia cancer cells treated with novel synthetic 1,2,3-triazole-chalcone conjugates. Bioorg Chem 2022; 123:105762. [DOI: 10.1016/j.bioorg.2022.105762] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022]
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15
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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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16
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Okunlola FO, Akawa OB, Soliman MES. Could the spanning of NAM-AD subsites by poly (ADP ribose) polymerase inhibitors potentiate their selective inhibitory activity in breast cancer treatment? Insight from biophysical computations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1994562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Felix O. Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Oluwole B. Akawa
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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17
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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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18
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Velagapudi UK, Patel BA, Shao X, Pathak SK, Ferraris DV, Talele TT. Recent development in the discovery of PARP inhibitors as anticancer agents: a patent update (2016-2020). Expert Opin Ther Pat 2021; 31:609-623. [PMID: 33554679 DOI: 10.1080/13543776.2021.1886275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Discovery of small molecules that impede the activity of single-strand DNA repair enzyme, PARP1, has led to four marketed drugs for the treatment of advanced-stage cancers. Hence, there is a renewed enthusiasm in the PARP inhibitor discovery arena. To reduce nonspecific interactions or potential toxicities, and to understand the role of other minimally explored PARP enzymes, exciting new findings have emerged toward the development of selective inhibitors and targeted chemical biology probes. Importantly, the conventional PARP inhibitor design has evolved in a way that could potentially lead to multienzyme-targeting - a polypharmacological approach against aggressive cancers. AREAS COVERED This review comprises recent progress made in the development of PARP inhibitors, primarily focused on human cancers. Discovery of novel PARP inhibitors with pan, selective, and multi-target inhibition using in vitro and in vivo cancer models is summarized and critically evaluated. Emphasis is given to patents published during 2016-2020, excluding TNKS 1/2 inhibitors. EXPERT OPINION The outstanding success demonstrated by the FDA approved PARP inhibitors has fueled further clinical evaluations for expansion of their clinical utilities. The current clinical investigations include new candidates as well as marketed PARP-targeted drugs, both as single agents and in combination with other chemotherapeutics. Recent advances have also unveiled critical roles of other PARPs in oncogenic signal transduction, in addition to those of the well-documented PARP1/2 and TNKS1/2 enzymes. Further studies on lesser-known PARP members are urgently needed for functional annotations and for understanding their roles in cancer progression and other human diseases.
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Affiliation(s)
- Uday Kiran Velagapudi
- Pace Analytical Life Sciences, LLC, Suite 102, 19 Presidential Way, Woburn, MA, 01801, USA
| | - Bhargav A Patel
- Department of Chemistry and Biochemistry, The University of Notre Dame, 329 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Xuwei Shao
- cFrontage Laboratories, Inc, 75 East Uwchlan Ave, Suite 100, Exton, PA, 19341, USA
| | - Sanjai Kumar Pathak
- dChemistry and Biochemistry Department, Queens College of the City University of New York, 65-30 Kissena Blvd., Flushing, NY, 11367, USA.,eChemistry Doctoral Program, Biochemistry Doctoral Program, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
| | - Dana V Ferraris
- fDepartment of Chemistry, McDaniel College, 2 College Hill, Westminster, MD, 21157, USA
| | - Tanaji T Talele
- gDepartment of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
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19
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Zuo X, Zhao H, Li D. Systematic inhibitor selectivity between PARP1 and PARP2 enzymes: Molecular implications for ovarian cancer personalized therapy. J Mol Recognit 2021; 34:e2891. [PMID: 33684965 DOI: 10.1002/jmr.2891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Human poly(ADP-ribose) polymerases (PARPs) are a class of nuclear enzymes involved in the pathogenesis of diverse gynecologic tumors. The PARP1 and PARP2 are the two most documented members in PARP family, which have been approved as the druggable targets of ovarian and cervical cancers. Selective targeting of the two enzymes with small-molecule inhibitors is a great challenge due to the high conservation in catalytic domain and active site. Here, we investigate the systematic selectivity profile of sophisticated PARP inhibitors between the two enzymes. Computational methods are used to model/optimize the complex structures of inhibitor ligands with PARP1/2 catalytic domains and then to estimate the theoretical Fenzymatic assays exhibit a good consistence with theoretical selectivity over six tested inhibitor samples (rc 2 = 0.857). It is revealed that the inhibitor selectivity is conferred from the exquisite difference in the residue composition and structural architecture of both the local activity sites and the whole catalytic domains of the two enzymes. In particular, the TMZ50 and ME0328 show strong selectivity between PARP1 and PARP2, but only the former has a potent activity on the two enzymes, whereas the latter can only inhibit the enzymes moderately. These compounds can be considered as potential lead molecular entities to develop new specific PARP-selective inhibitor drugs for personalized therapy combating gynecologic cancers.
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Affiliation(s)
- Xueqian Zuo
- Department of Gynaecology, Cangzhou People's Hospital Affiliated to Cangzhou Medical College, Cangzhou, China
| | - Haibo Zhao
- Department of Gynaecology, Cangzhou People's Hospital Affiliated to Cangzhou Medical College, Cangzhou, China
| | - Dan Li
- Department of Gynaecology, Cangzhou People's Hospital Affiliated to Cangzhou Medical College, Cangzhou, China
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20
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Ogden TEH, Yang JC, Schimpl M, Easton LE, Underwood E, Rawlins P, McCauley M, Langelier MF, Pascal J, Embrey K, Neuhaus D. Dynamics of the HD regulatory subdomain of PARP-1; substrate access and allostery in PARP activation and inhibition. Nucleic Acids Res 2021; 49:2266-2288. [PMID: 33511412 PMCID: PMC7913765 DOI: 10.1093/nar/gkab020] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/17/2020] [Accepted: 01/08/2021] [Indexed: 01/08/2023] Open
Abstract
PARP-1 is a key early responder to DNA damage in eukaryotic cells. An allosteric mechanism links initial sensing of DNA single-strand breaks by PARP-1's F1 and F2 domains via a process of further domain assembly to activation of the catalytic domain (CAT); synthesis and attachment of poly(ADP-ribose) (PAR) chains to protein sidechains then signals for assembly of DNA repair components. A key component in transmission of the allosteric signal is the HD subdomain of CAT, which alone bridges between the assembled DNA-binding domains and the active site in the ART subdomain of CAT. Here we present a study of isolated CAT domain from human PARP-1, using NMR-based dynamics experiments to analyse WT apo-protein as well as a set of inhibitor complexes (with veliparib, olaparib, talazoparib and EB-47) and point mutants (L713F, L765A and L765F), together with new crystal structures of the free CAT domain and inhibitor complexes. Variations in both dynamics and structures amongst these species point to a model for full-length PARP-1 activation where first DNA binding and then substrate interaction successively destabilise the folded structure of the HD subdomain to the point where its steric blockade of the active site is released and PAR synthesis can proceed.
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Affiliation(s)
- Tom E H Ogden
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Michael M McCauley
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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21
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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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22
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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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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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24
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Li S, Li XY, Zhang TJ, Zhu J, Xue WH, Qian XH, Meng FH. Design, synthesis and biological evaluation of erythrina derivatives bearing a 1,2,3-triazole moiety as PARP-1 inhibitors. Bioorg Chem 2020; 96:103575. [DOI: 10.1016/j.bioorg.2020.103575] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/15/2022]
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25
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Sosa-Rivadeneyra MV, Venkatesan P, Flores-Manuel F, Bernès S, Höpfl H, Cerón M, Thamotharan S, Percino MJ. Quantitative analysis of intermolecular interactions in cocrystals and a pair of polymorphous cocrystal hydrates from 1,4-dihydroquinoxaline-2,3-dione and 1 H-benzo[ d]imidazol-2(3 H)-one with 2,5-dihydroxy-1,4-benzoquinones: a combined X-ray structural and theoretical analysis. CrystEngComm 2020. [DOI: 10.1039/d0ce01056a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Study and quantification of intermolecular interactions in five cocrystals and cocrystals hydrates by PIXEL, DFT, Hirshfeld surface and QTAIM calculations.
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Affiliation(s)
| | - Perumal Venkatesan
- Unidad de Polímeros y Electrónica Orgánica
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla
- Puebla
- Mexico
| | - Fermin Flores-Manuel
- Facultad de Ciencias Químicas
- Benemérita Universidad Autónoma de Puebla (BUAP)
- Puebla
- Mexico
| | - Sylvain Bernès
- Instituto de Física
- Benemérita Universidad Autónoma de Puebla (IFBUAP)
- Puebla
- Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas
- Instituto de Investigación en Ciencias Básicas y Aplicadas
- Universidad Autónoma del Estado de Morelos
- Cuernavaca
- Mexico
| | - Margarita Cerón
- Unidad de Polímeros y Electrónica Orgánica
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla
- Puebla
- Mexico
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur
| | - M. Judith Percino
- Unidad de Polímeros y Electrónica Orgánica
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla
- Puebla
- Mexico
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Yang H, Gao Y, Fan X, Liu X, Peng L, Ci X. Oridonin Sensitizes Cisplatin-Induced Apoptosis via AMPK/Akt/mTOR-Dependent Autophagosome Accumulation in A549 Cells. Front Oncol 2019; 9:769. [PMID: 31475112 PMCID: PMC6702493 DOI: 10.3389/fonc.2019.00769] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/30/2019] [Indexed: 01/04/2023] Open
Abstract
AMPK-mediated autophagy and Akt/mTOR pathways play important roles in current cancer treatments. Oridonin (Ori), an ent-kaurane diterpenoid isolated from Isodon rubescens, exerts extensive anti-tumor potential and controversial effects on autophagy. In this study, we investigated the effect of Ori on the autophagy, apoptosis, and AMPK/Akt/mTOR pathways and determined whether Ori was related to the increased cisplatin sensitivity observed in A549 cells. First, we found that Ori suppressed Akt/mTOR, Bcl2 and autophagy flux with enhanced levels of Atg3, P62, and LC3II, which was also shown as the accumulation of autophagosomes. AMPK and pro-apoptotic proteins (caspase3, Bax, and PARP) were activated in Ori-treated cells. With the pretreatment of compound c (AMPK inhibitor), the activation of autophagosomes, apoptosis and the inhibition of Akt/mTOR pathways induced by Ori were all reversed. The Ori-activated apoptosis-related markers mentioned previously and the cell-killing effect were restrained by 3-MA (inhibitor of autophagosomes) treatment. Therefore, we hypothesized that the Ori-induced pro-apoptotic effect was mediated by AMPK/Akt/mTOR-dependent accumulation of impaired autophagosomes. Furthermore, Ori could increase the sensitivity of cisplatin through its increased cell-killing, autophagy-suppressing and apoptosis-inducing activities. In addition to sensitizing cisplatin, Ori also alleviated cisplatin-induced acute renal injury in vivo, manifested as depleted BUN, CRE, kidney index, and weight loss compared to the cisplatin group. In summary, apart from its protective effect on cisplatin-induced nephrotoxicity, Ori enhanced cisplatin sensitivity via its pro-apoptotic activity mediated by AMPK/Akt/mTOR-dependent autophagosome activation, which may be a potential therapeutic target for non-small cell lung cancer.
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Affiliation(s)
- Huahong Yang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yun Gao
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xiaoye Fan
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xingkai Liu
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, China
| | - Liping Peng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xinxin Ci
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
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