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Roggia M, Natale B, Amendola G, Grasso N, Di Maro S, Taliani S, Castellano S, Reina SCR, Salvati E, Amato J, Cosconati S. Discovering Dually Active Anti-cancer Compounds with a Hybrid AI-structure-based Approach. J Chem Inf Model 2024. [PMID: 39276072 DOI: 10.1021/acs.jcim.4c01132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2024]
Abstract
Cancer's persistent growth often relies on its ability to maintain telomere length and tolerate the accumulation of DNA damage. This study explores a computational approach to identify compounds that can simultaneously target both G-quadruplex (G4) structures and poly(ADP-ribose) polymerase (PARP)1 enzyme, offering a potential multipronged attack on cancer cells. We employed a hybrid virtual screening (VS) protocol, combining the power of machine learning with traditional structure-based methods. PyRMD, our AI-powered tool, was first used to analyze vast chemical libraries and to identify potential PARP1 inhibitors based on known bioactivity data. Subsequently, a structure-based VS approach selected compounds from these identified inhibitors for their G4 stabilization potential. This two-step process yielded 50 promising candidates, which were then experimentally validated for their ability to inhibit PARP1 and stabilize G4 structures. Ultimately, four lead compounds emerged as promising candidates with the desired dual activity and demonstrated antiproliferative effects against specific cancer cell lines. This study highlights the potential of combining Artificial Intelligence and structure-based methods for the discovery of multitarget anticancer compounds, offering a valuable approach for future drug development efforts.
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Affiliation(s)
- Michele Roggia
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Benito Natale
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Giorgio Amendola
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy
| | - Salvatore Di Maro
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Sabrina Castellano
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano Salerno, Italy
| | | | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
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Huang Y, Zhu T, Li Y, Huang D. Chain Extension of Piperazine in Ethanol: Synthesis of 2-(4-(2-(Phenylthio)ethyl)piperazinyl)acetonitriles and ACAT-1 Inhibitors. Molecules 2024; 29:3723. [PMID: 39202802 PMCID: PMC11356844 DOI: 10.3390/molecules29163723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
A base-induced synthesis of 2-(4-(2-(phenylthio)ethyl)piperazinyl) acetonitriles by reaction of disulfides, 1-(chloromethyl)-4-aza-1-azonia bicyclo[2.2.2]octane chloride and trimethylsilyl cyanide is reported. The scope of the method is demonstrated with 30 examples. The reaction mechanism research indicates that the three-component reaction would be a SN2 reaction. The products exhibit good activities towards advanced synthesis of aqueous soluble acyl-CoA: cholesterol O-acyltransferase-1 (ACAT-1) inhibitors. Our work is superior as it uses less-odor disulfides as carbon sources and EtOH as solvent in a water and dioxygen insensitive reaction system, followed by a simple purification process.
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Affiliation(s)
- Ying Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350002, China; (Y.H.); (T.Z.)
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350007, China
- Fujian College, University of Chinese Academy of Sciences, Fuzhou 350002, China
| | - Tingyu Zhu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350002, China; (Y.H.); (T.Z.)
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350007, China
- Fujian College, University of Chinese Academy of Sciences, Fuzhou 350002, China
| | - Yinghua Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350002, China; (Y.H.); (T.Z.)
| | - Deguang Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350002, China; (Y.H.); (T.Z.)
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Ai D, Wu J, Cai H, Zhao D, Chen Y, Wei J, Xu J, Zhang J, Wang L. A multi-task FP-GNN framework enables accurate prediction of selective PARP inhibitors. Front Pharmacol 2022; 13:971369. [PMID: 36304149 PMCID: PMC9592829 DOI: 10.3389/fphar.2022.971369] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 08/16/2024] Open
Abstract
PARP (poly ADP-ribose polymerase) family is a crucial DNA repair enzyme that responds to DNA damage, regulates apoptosis, and maintains genome stability; therefore, PARP inhibitors represent a promising therapeutic strategy for the treatment of various human diseases including COVID-19. In this study, a multi-task FP-GNN (Fingerprint and Graph Neural Networks) deep learning framework was proposed to predict the inhibitory activity of molecules against four PARP isoforms (PARP-1, PARP-2, PARP-5A, and PARP-5B). Compared with baseline predictive models based on four conventional machine learning methods such as RF, SVM, XGBoost, and LR as well as six deep learning algorithms such as DNN, Attentive FP, MPNN, GAT, GCN, and D-MPNN, the evaluation results indicate that the multi-task FP-GNN method achieves the best performance with the highest average BA, F1, and AUC values of 0.753 ± 0.033, 0.910 ± 0.045, and 0.888 ± 0.016 for the test set. In addition, Y-scrambling testing successfully verified that the model was not results of chance correlation. More importantly, the interpretability of the multi-task FP-GNN model enabled the identification of key structural fragments associated with the inhibition of each PARP isoform. To facilitate the use of the multi-task FP-GNN model in the field, an online webserver called PARPi-Predict and its local version software were created to predict whether compounds bear potential inhibitory activity against PARPs, thereby contributing to design and discover better selective PARP inhibitors.
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Affiliation(s)
- Daiqiao Ai
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Jingxing Wu
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Hanxuan Cai
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Duancheng Zhao
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Yihao Chen
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Jiajia Wei
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
| | - Jianrong Xu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiquan Zhang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang, China
| | - Ling Wang
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou, China
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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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Guha S, Yussif El‐Deeb I, Yadav S, Das R, Dutta Dubey K, Baruah M, Ludovic G, Sen S. Capturing a Pentacyclic Fragment‐Based Library Derived from Perophoramidine: Their Design, Synthesis and Evaluation as Anticancer Compounds by DNA Double‐Strand Breaks (DSB) and PARP‐1 Inhibition. Chemistry 2022; 28:e202202405. [DOI: 10.1002/chem.202202405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Souvik Guha
- Department of Chemistry School of Natural Sciences Shiv Nadar University, Delhi NCR
| | | | - Shalini Yadav
- Department of Chemistry School of Natural Sciences Shiv Nadar University, Delhi NCR
| | - Ranajit Das
- Department of Chemistry School of Natural Sciences Shiv Nadar University, Delhi NCR
| | | | - Mousumi Baruah
- Department of Chemistry School of Natural Sciences Shiv Nadar University, Delhi NCR
| | - Gremaud Ludovic
- School of Engineering and Architecture Institute of Chemical Technology at University of Applied Sciences and Arts of Western Mumbai, Switzerland 1700 Fribourg Switzerland
| | - Subhabrata Sen
- Department of Chemistry School of Natural Sciences Shiv Nadar University, Delhi NCR
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Kayumov M, Jia L, Pardaev A, Song SS, Mirzaakhmedov S, Ding C, Cheng YJ, Zhang R(I, Bao X, Miao ZH, He JX, Zhang A. Design, synthesis and pharmacological evaluation of new PARP1 inhibitors by merging pharmacophores of olaparib and the natural product alantolactone. Eur J Med Chem 2022; 240:114574. [DOI: 10.1016/j.ejmech.2022.114574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/14/2022] [Accepted: 06/25/2022] [Indexed: 11/04/2022]
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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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Okunlola FO, Akawa OB, Subair TI, Omolabi KF, Soliman MES. Unravelling the Mechanistic Role of Quinazolinone Pharmacophore in the Inhibitory Activity of Bis-quinazolinone Derivative on Tankyrase-1 in the Treatment of Colorectal Cancer (CRC) and Non-small Cell Lung Cancer (NSCLC): A Computational Approach. Cell Biochem Biophys 2021; 80:1-10. [PMID: 34453681 DOI: 10.1007/s12013-021-01027-3] [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] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
In recent years, tankyrase inhibition has gained a great focus as an anti-cancer strategy due to their modulatory effect on WNT/β-catenin pathway implicated in many malignancies, including colorectal cancer (CRC) and non-small cell lung cancer (NSCLC). Based on the structural homology in the catalytic domain of PARP enzymes, bis-quinazolinone 5 (Cpd 5) was designed to be a potent selective tankyrase inhibitor. In this study, we employed molecular dynamics simulations and binding energy analysis to decipher the underlying mechanism of TNK-1 inhibition by Cpd 5 in comparison with a known selective tankyrase, IWR-1. The Cpd 5 had a relatively higher ΔGbind than IWR-1 from the thermodynamics analysis, revealing the better inhibitory activity of Cpd 5 compared to IWR-1. High involvement of solvation energy (ΔGsol) and the van der Waals energy (ΔEvdW) potentiated the affinity of Cpd 5 at TNK-1 active site. Interestingly, the keto group and the N3 atom of the quinazolinone nucleus of Cpd 5, occupying the NAM subsite, was able to form H-bond with Gly1185, thereby favoring the better stability and higher inhibitory efficacy of Cpd 5 relative to IWR-1. Our analysis proved that the firm binding of Cpd 5 was achieved by the quinazolinone groups via the hydrophobic interactions with the side chains of key site residues at the two subsite regions: His1201, Phe1188, Ala1191, and Ile1192 at the AD subsite and Tyr1224, Tyr1213, and Ala1215 at the NAM subsite. Thus, Cpd 5 is dominantly bound through π-π stacked interactions and other hydrophobic interactions. We believe that findings from this study would provide an important rationale towards the structure-based design of improved selective tankyrase inhibitors in cancer therapy.
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Affiliation(s)
- Felix O Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Oluwole B Akawa
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Temitayo I Subair
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Kehinde F Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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