1
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Gogoi U, Gogoi N, Rajkhowa S, Khan SA, Daffa Alla Omer Hajedris N, Al-Hoshani N, Al-Shouli ST, Das A. Expanding the therapeutic arsenal against cancer: a computational investigation of hybrid xanthone derivatives as selective Topoisomerase 2α ATPase inhibitors. J Biomol Struct Dyn 2023:1-30. [PMID: 37975405 DOI: 10.1080/07391102.2023.2280723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The DNA topoisomerase II (topo II) enzyme plays an important role in the replication, recombination, and repair of DNA. Despite their widespread applications in cancer therapy, new, selective, and potent topo II inhibitors with better pharmaceutical profiles are needed to handle drug resistance and severe adverse effects. In this respect, an array of 36 new anticancer compounds was designed based on a Xanthone core tethered to multifunctional Pyridine-amines and Imidazole scaffold via alkyl chain linkers. An integrated in silico approach was used to understand the structural basis and mechanism of inhibition of the hybrid xanthone derivatives. In this study, we established an initial virtual screening workflow based on pharmacophore mapping, docking, and cancer target association to validate the target selection process. Next, a simulation-based docking was conducted along with pharmacokinetic analysis to filter out the five best compounds (7, 10, 25, 27, and 30) having binding energies within the range of -60.45 to -40.97 kcal/mol. The screened compounds were further subjected to molecular dynamics simulation for 200 ns followed by MM-GBSA and ligand properties analysis to assess the stability and binding affinity to hTOP2α. The top-ranking hits 3,7-bis(3-(2-aminopyridin-3-ylhydroxy)propoxy)-1-hydroxy-9H-xanthen-9-one (ligand 7) and 3,8-bis(3-(2-aminopyridin-3-ylhydroxy)propoxy)-1-hydroxy-9H-xanthen-9-one (ligand 25) were found to have no toxicity, optimum pharmacokinetic and, DFT properties and stable intermolecular interactions with the active site of hTopo IIα protein. In conclusion, further in vitro and in vivo experimental validation of the identified lead molecules is warranted for the discovery of new human Topoisomerase 2 alpha inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urvashee Gogoi
- Department of Pharmaceutical Sciences, Faculty of Science & Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Faculty of Science & Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Shah Alam Khan
- College of Pharmacy, National University of Science and Technology, Muscat, Oman
| | - Nisreen Daffa Alla Omer Hajedris
- College of Medicine, Basic Medical Department, Almaarefa University, Riyadh, Saudi Arabia
- Faculty of Medicine, Department of Physiology, Khartoum University, Khartoum, Sudan
| | - Nawal Al-Hoshani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samia T Al-Shouli
- Immunology Unit, Pathology department, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Aparoop Das
- Department of Pharmaceutical Sciences, Faculty of Science & Engineering, Dibrugarh University, Dibrugarh, Assam, India
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2
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Basagni F, Marotta G, Rosini M, Minarini A. Polyamine-Drug Conjugates: Do They Boost Drug Activity? Molecules 2023; 28:molecules28114518. [PMID: 37298993 DOI: 10.3390/molecules28114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Over the past two decades, the strategy of conjugating polyamine tails with bioactive molecules such as anticancer and antimicrobial agents, as well as antioxidant and neuroprotective scaffolds, has been widely exploited to enhance their pharmacological profile. Polyamine transport is elevated in many pathological conditions, suggesting that the polyamine portion could improve cellular and subcellular uptake of the conjugate via the polyamine transporter system. In this review, we have presented a glimpse on the polyamine conjugate scenario, classified by therapeutic area, of the last decade with the aim of highlighting achievements and fostering future developments.
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Affiliation(s)
- Filippo Basagni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Giambattista Marotta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Michela Rosini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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3
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Shen R, Chen Y, Wu J, Zhao L, Yang A, Kou X. Effect of Bis-Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone. Chem Biodivers 2022; 19:e202101021. [PMID: 35324082 DOI: 10.1002/cbdv.202101021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
A bis-dimethylamine substituted xanthone (Xan-2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6-trihydroxyxanthone (Xan-1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan-1 and Xan-2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan-2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan-2 exhibited higher DNA binding affinity than Xan-1. Further study showed that Xan-2 could inhibit the proliferation of HeLa, SGC-7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan-2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.
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Affiliation(s)
- Rui Shen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuhong Chen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jianhua Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lihua Zhao
- Tianjin Renai College, Tianjin, 301636, China
| | - Aihong Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xiaodi Kou
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
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4
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Synthesis and biological evaluation of xanthone derivatives as anti-cancer agents targeting topoisomerase II and DNA. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02862-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Kurniawan YS, Priyangga KTA, Jumina, Pranowo HD, Sholikhah EN, Zulkarnain AK, Fatimi HA, Julianus J. An Update on the Anticancer Activity of Xanthone Derivatives: A Review. Pharmaceuticals (Basel) 2021; 14:1144. [PMID: 34832926 PMCID: PMC8625896 DOI: 10.3390/ph14111144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
The annual number of cancer deaths continues increasing every day; thus, it is urgent to search for and find active, selective, and efficient anticancer drugs as soon as possible. Among the available anticancer drugs, almost all of them contain heterocyclic moiety in their chemical structure. Xanthone is a heterocyclic compound with a dibenzo-γ-pyrone framework and well-known to have "privileged structures" for anticancer activities against several cancer cell lines. The wide anticancer activity of xanthones is produced by caspase activation, RNA binding, DNA cross-linking, as well as P-gp, kinase, aromatase, and topoisomerase inhibition. This anticancer activity depends on the type, number, and position of the attached functional groups in the xanthone skeleton. This review discusses the recent advances in the anticancer activity of xanthone derivatives, both from natural products isolation and synthesis methods, as the anticancer agent through in vitro, in vivo, and clinical assays.
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Affiliation(s)
- Yehezkiel Steven Kurniawan
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Krisfian Tata Aneka Priyangga
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Jumina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Eti Nurwening Sholikhah
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;
| | - Abdul Karim Zulkarnain
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (A.K.Z.); (H.A.F.)
| | - Hana Anisa Fatimi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (A.K.Z.); (H.A.F.)
| | - Jeffry Julianus
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Sanata Dharma, Yogyakarta 55282, Indonesia;
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6
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Kharb R. Updates on Receptors Targeted by Heterocyclic Scaffolds: New Horizon in Anticancer Drug Development. Anticancer Agents Med Chem 2021; 21:1338-1349. [PMID: 32560614 DOI: 10.2174/1871520620666200619181102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 11/22/2022]
Abstract
Anticancer is a high priority research area for scientists as cancer is one of the leading causes of death globally. It is pertinent to mention here that conventional anticancer drugs such as methotrexate, vincristine, cyclophosphamide, etoposide, doxorubicin, cisplatin, etc. are not much efficient for the treatment of different types of cancer; also these suffer from serious side effects leading to therapy failure. A large variety of cancerrelated receptors such as carbonic anhydrase, tyrosine kinase, topoisomerase, protein kinase, histone deacetylase, etc. have been identified which can be targeted by anticancer drugs. Heterocycles like oxadiazole, thiazole, thiadiazole, indole, pyridine, pyrimidine, benzimidazole, etc. play a pivotal role in modern medicinal chemistry because they have a broad spectrum of pharmacological activities including prominent anticancer activity. Therefore, it was considered significant to explore heterocyclic compounds reported in recent most literature which can bind effectively with the cancer-related receptors. This will not only provide a targeted approach to deal with cancer but also the safety profile of the drugs can be further improved. The information provided in this manuscript may be found useful for the design and development of anticancer drugs.
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Affiliation(s)
- Rajeev Kharb
- Centre for Pharmaceutical Chemistry & Pharmaceutical Analysis, Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida-201313, Uttar Pradesh, India
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7
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Vann KR, Oviatt AA, Osheroff N. Topoisomerase II Poisons: Converting Essential Enzymes into Molecular Scissors. Biochemistry 2021; 60:1630-1641. [PMID: 34008964 PMCID: PMC8209676 DOI: 10.1021/acs.biochem.1c00240] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The extensive length, compaction, and interwound nature of DNA, together with its controlled and restricted movement in eukaryotic cells, create a number of topological issues that profoundly affect all of the functions of the genetic material. Topoisomerases are essential enzymes that modulate the topological structure of the double helix, including the regulation of DNA under- and overwinding and the removal of tangles and knots from the genome. Type II topoisomerases alter DNA topology by generating a transient double-stranded break in one DNA segment and allowing another segment to pass through the DNA gate. These enzymes are involved in a number of critical nuclear processes in eukaryotic cells, such as DNA replication, transcription, and recombination, and are required for proper chromosome structure and segregation. However, because type II topoisomerases generate double-stranded breaks in the genetic material, they also are intrinsically dangerous enzymes that have the capacity to fragment the genome. As a result of this dualistic nature, type II topoisomerases are the targets for a number of widely prescribed anticancer drugs. This article will describe the structure and catalytic mechanism of eukaryotic type II topoisomerases and will go on to discuss the actions of topoisomerase II poisons, which are compounds that stabilize DNA breaks generated by the type II enzyme and convert these essential enzymes into "molecular scissors." Topoisomerase II poisons represent a broad range of structural classes and include anticancer drugs, dietary components, and environmental chemicals.
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Affiliation(s)
- Kendra R Vann
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alexandria A Oviatt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Departments of Biochemistry and Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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8
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Chen JN, Wu XK, Lu CH, Li X. Structure-activity relationship of novel acridone derivatives as antiproliferative agents. Bioorg Med Chem 2021; 29:115868. [PMID: 33191085 DOI: 10.1016/j.bmc.2020.115868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 10/23/2022]
Abstract
Unlike other DNA topoisomerase II (topo II) inhibitors, our recently identified acridone derivative E17 exerted strong cytotoxic activity by inhibiting topo II without causing topo II degradation and DNA damage, which promoted us to explore more analogues of E17 by expanding its chemical diversification and enrich the structure-activity relationship (SAR) outcomes of acridone-oriented chemotypes. To achieve this goal, 42 novel acridone derivatives were synthesized and evaluated for their antiproliferative efficacies. SAR investigations revealed that orientation and spatial topology of R3 substituents make greater contributions to the bioactivity, exemplified by compounds E24, E25 and E27, which has provided valuable information for guiding further development of acridone derivatives as promising drug candidates.
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Affiliation(s)
- Ji-Ning Chen
- Key Laboratory of Chemistry and Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, PR China
| | - Xing-Kang Wu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Chun-Hua Lu
- Key Laboratory of Chemistry and Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, PR China
| | - Xun Li
- Key Laboratory of Chemistry and Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, PR China; Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250002, PR China
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9
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Ortega JA, Arencibia JM, Minniti E, Byl JAW, Franco-Ulloa S, Borgogno M, Genna V, Summa M, Bertozzi SM, Bertorelli R, Armirotti A, Minarini A, Sissi C, Osheroff N, De Vivo M. Novel, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II α over β. J Med Chem 2020; 63:12873-12886. [PMID: 33079544 PMCID: PMC7668297 DOI: 10.1021/acs.jmedchem.0c00774] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
We disclose a novel
class of 6-amino-tetrahydroquinazoline derivatives
that inhibit human topoisomerase II (topoII), a validated target of
anticancer drugs. In contrast to topoII-targeted drugs currently in
clinical use, these compounds do not act as topoII poisons that enhance
enzyme-mediated DNA cleavage, a mechanism that is linked to the development
of secondary leukemias. Instead, these tetrahydroquinazolines block
the topoII function with no evidence of DNA intercalation. We identified
a potent lead compound [compound 14 (ARN-21934) IC50 = 2 μM for inhibition of DNA relaxation, as compared
to an IC50 = 120 μM for the anticancer drug etoposide]
with excellent metabolic stability and solubility. This new compound
also shows ~100-fold selectivity for topoIIα over topoβ,
a broad antiproliferative activity toward cultured human cancer cells,
a favorable in vivo pharmacokinetic profile, and the ability to penetrate
the blood–brain barrier. Thus, ARN-21934 is a highly promising
lead for the development of novel and potentially safer topoII-targeted
anticancer drugs.
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Affiliation(s)
- Jose Antonio Ortega
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose M Arencibia
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Elirosa Minniti
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Sebastian Franco-Ulloa
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marco Borgogno
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Maria Summa
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6307, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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10
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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11
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Arencibia JM, Brindani N, Franco-Ulloa S, Nigro M, Kuriappan JA, Ottonello G, Bertozzi SM, Summa M, Girotto S, Bertorelli R, Armirotti A, De Vivo M. Design, Synthesis, Dynamic Docking, Biochemical Characterization, and in Vivo Pharmacokinetics Studies of Novel Topoisomerase II Poisons with Promising Antiproliferative Activity. J Med Chem 2020; 63:3508-3521. [PMID: 32196342 PMCID: PMC7997578 DOI: 10.1021/acs.jmedchem.9b01760] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
We
previously reported a first set of hybrid topoisomerase II (topoII)
poisons whose chemical core merges key pharmacophoric elements of
etoposide and merbarone, which are two well-known topoII blockers.
Here, we report on the expansion of this hybrid molecular scaffold
and present 16 more hybrid derivatives that have been designed, synthesized,
and characterized for their ability to block topoII and for their
overall drug-like profile. Some of these compounds act as topoII poison
and exhibit good solubility, metabolic (microsomal) stability, and
promising cytotoxicity in three cancer cell lines (DU145, HeLa, A549).
Compound 3f (ARN24139) is the most promising drug-like
candidate, with a good pharmacokinetics profile in vivo. Our results indicate that this hybrid new chemical class of topoII
poisons deserves further exploration and that 3f is a
favorable lead candidate as a topoII poison, meriting future studies
to test its efficacy in in vivo tumor models.
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Affiliation(s)
- Jose M Arencibia
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Michela Nigro
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Giuliana Ottonello
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Maria Summa
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Stefania Girotto
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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12
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Almansour AI, Kumar RS, Arumugam N, Bianchini G, Menéndez JC, Mohammad F, Dupadahalli K, Altaf M. D-Ring-Modified Analogues of Luotonin A with Reduced Planarity: Design, Synthesis, and Evaluation of Their Topoisomerase Inhibition-Associated Cytotoxicity. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2514524. [PMID: 31815127 PMCID: PMC6877907 DOI: 10.1155/2019/2514524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022]
Abstract
A- and D-ring-modified luotonin-inspired heterocycles have been synthesized and were evaluated for their activity against the viability of four cancer cell lines in vitro, namely, MCF7, HCT116, JURKAT, and NCI-H460. The analysis of results indicated that two of the synthesized derivatives displayed good inhibition against the growth of the human colon cancer HCT116 cell line, with potencies lower than but in the same order of magnitude as camptothecin (CPT). These two luotonin analogues also showed an activity similar to that of the highly potent alkaloid CPT as inhibitors of topoisomerase I and also inhibited topoisomerase II. These results show that complete planarity is not a strict requirement for topoisomerase inhibition by luotonin-related compounds, paving the way to the design of analogues with improved solubility.
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Affiliation(s)
- Abdulrahman I. Almansour
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Giulia Bianchini
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain
| | - J. Carlos Menéndez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain
| | - Faruq Mohammad
- Surfactants Research Chair, Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Kotresha Dupadahalli
- Department of Botany, Davangere University, Shivagangothri, Davangere 577007, Karnataka, India
| | - Mohammad Altaf
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
- Central Laboratory, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
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Yu L, Chen L, Luo G, Liu L, Zhu W, Yan P, Zhang P, Zhang C, Wu W. Study on Synthesis and Biological Evaluation of 3-Aryl Substituted Xanthone Derivatives as Novel and Potent Tyrosinase Inhibitors. Chem Pharm Bull (Tokyo) 2019; 67:1232-1241. [DOI: 10.1248/cpb.c19-00572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lihong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Liandi Chen
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
- The Third Affiliated Hospital of Guangzhou Medical University
| | - Guolin Luo
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Licai Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Wenqi Zhu
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Pengke Yan
- The Third Affiliated Hospital of Guangzhou Medical University
| | - Peiquan Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Chao Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
| | - Wenhao Wu
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University
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14
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Rosini M, Simoni E, Caporaso R, Basagni F, Catanzaro M, Abu IF, Fagiani F, Fusco F, Masuzzo S, Albani D, Lanni C, Mellor IR, Minarini A. Merging memantine and ferulic acid to probe connections between NMDA receptors, oxidative stress and amyloid-β peptide in Alzheimer's disease. Eur J Med Chem 2019; 180:111-120. [DOI: 10.1016/j.ejmech.2019.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022]
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15
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Kuriappan JA, Osheroff N, De Vivo M. Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II. J Chem Inf Model 2019; 59:4007-4017. [PMID: 31449404 PMCID: PMC6800198 DOI: 10.1021/acs.jcim.9b00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Human
type II topoisomerases (TopoII) are essential for controlling
DNA topology within the cell. For this reason, there are a number
of TopoII-targeted anticancer drugs that act by inducing DNA cleavage
mediated by both TopoII isoforms (TopoIIα and TopoIIβ)
in cells. However, recent studies suggest that specific poisoning
of TopoIIα may be a safer strategy for treating cancer. This
is because poisoning of TopoIIβ appears to be linked to the
generation of secondary leukemia in patients. We recently reported
that enzyme-mediated DNA cleavage complexes (in which TopoII is covalently
linked to the cleaved DNA during catalysis) formed in the presence
of the anticancer drug etoposide persisted approximately 3-fold longer
with TopoIIα than TopoIIβ. Notably, enhanced drug-target
residence time may reduce the adverse effects of specific TopoIIα
poisons. However, it is still not clear how to design drugs that are
specific for the α isoform. In this study, we report the results
of classical molecular dynamics (MD) simulations to comparatively
analyze the molecular interactions formed within the TopoII/DNA/etoposide
complex with both isoforms. We also used smoothed potential MD to
estimate etoposide dissociation kinetics from the two isoform complexes.
These extensive classical and enhanced sampling simulations revealed
stabilizing interactions of etoposide with two serine residues (Ser763
and Ser800) in TopoIIα. These interactions are missing in TopoIIβ,
where both amino acids are alanine residues. This may explain the
greater persistence of etoposide-stabilized cleavage complexes formed
with Topo TopoIIα. These findings could be useful for the rational
design of specific TopoIIα poisons.
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Affiliation(s)
- Jissy A Kuriappan
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Neil Osheroff
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Medicine (Hematology/Oncology) , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-6307 , United States.,VA Tennessee Valley Healthcare System , Nashville , Tennessee 37212 , United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
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16
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Synthesis and biological evaluation of novel carbazole-rhodanine conjugates as topoisomerase II inhibitors. Bioorg Med Chem Lett 2018; 28:1320-1323. [DOI: 10.1016/j.bmcl.2018.03.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 12/18/2022]
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17
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Wu G, Qi X, Mo X, Yu G, Wang Q, Zhu T, Gu Q, Liu M, Li J, Li D. Structure-based discovery of cytotoxic dimeric tetrahydroxanthones as potential topoisomerase I inhibitors from a marine-derived fungus. Eur J Med Chem 2018; 148:268-278. [PMID: 29466776 DOI: 10.1016/j.ejmech.2018.02.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 10/18/2022]
Abstract
DNA topoisomerase I (Topo I) is an important anticancer drug target, and xanthone dimers are considered to be a new kind of Topo I inhibitor chemotypes. Based on the characteristics of dimeric xanthone structures, five new dimeric xanthones (1-5) and two known SAD isomers (6 and 7) were isolated from the mangrove-derived fungus Aspergillus vericolor. The absolute configurations of compounds 1-7, entailing both central and axial chirality elements, were established by a combination of ECD comparison, chemical conversions, and biogenetic considerations. Compounds 1-7 possessed high structural diversity and exhibited cytotoxicity at different levels. The selected new compounds 1, 2, and 5 showed Topo I inhibition properties and the most potent compound 1, an atropisomer of compound 2, was confirmed to inhibit Topo I-mediated DNA relaxation by targeting Topo I, thereby, arresting the cell cycle process and inducing necrosis in cancer cells. Molecular docking studies showed that compound 1 could bind DNA by π-π interaction and DNA Topo I by hydrogen bonds to form a ternary complex.
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Affiliation(s)
- Guangwei Wu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China
| | - Xiaomei Mo
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China
| | - Guihong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Qiang Wang
- College of Pharmacy, South Central University for Nationalities, Wuhan, 430074, PR China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Ming Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
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18
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Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
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