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Wu Z, Chen S, Wang Y, Li F, Xu H, Li M, Zeng Y, Wu Z, Gao Y. Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis. Int J Surg 2024; 110:3848-3878. [PMID: 38502850 PMCID: PMC11175770 DOI: 10.1097/js9.0000000000001289] [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: 11/08/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
AIM Computer-aided drug design (CADD) is a drug design technique for computing ligand-receptor interactions and is involved in various stages of drug development. To better grasp the frontiers and hotspots of CADD, we conducted a review analysis through bibliometrics. METHODS A systematic review of studies published between 2000 and 20 July 2023 was conducted following the PRISMA guidelines. Literature on CADD was selected from the Web of Science Core Collection. General information, publications, output trends, countries/regions, institutions, journals, keywords, and influential authors were visually analyzed using software such as Excel, VOSviewer, RStudio, and CiteSpace. RESULTS A total of 2031 publications were included. These publications primarily originated from 99 countries or regions led by the U.S. and China. Among the contributors, MacKerell AD had the highest number of articles and the greatest influence. The Journal of Medicinal Chemistry was the most cited journal, whereas the Journal of Chemical Information and Modeling had the highest number of publications. CONCLUSIONS Influential authors in the field were identified. Current research shows active collaboration between countries, institutions, and companies. CADD technologies such as homology modeling, pharmacophore modeling, quantitative conformational relationships, molecular docking, molecular dynamics simulation, binding free energy prediction, and high-throughput virtual screening can effectively improve the efficiency of new drug discovery. Artificial intelligence-assisted drug design and screening based on CADD represent key topics that will influence future development. Furthermore, this paper will be helpful in better understanding the frontiers and hotspots of CADD.
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Affiliation(s)
- Zhenhui Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Shupeng Chen
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Yihao Wang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Fangyang Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Huanhua Xu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Maoxing Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Yingjian Zeng
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Zhenfeng Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Yue Gao
- School of Pharmacy, Jiangxi University of Chinese Medicine
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
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Alajroush DR, Smith CB, Anderson BF, Oyeyemi IT, Beebe SJ, Holder AA. A Comparison of In Vitro Studies between Cobalt(III) and Copper(II) Complexes with Thiosemicarbazone Ligands to Treat Triple Negative Breast Cancer. Inorganica Chim Acta 2024; 562:121898. [PMID: 38282819 PMCID: PMC10810091 DOI: 10.1016/j.ica.2023.121898] [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] [Indexed: 01/30/2024]
Abstract
Metal complexes have gained significant attention as potential anti-cancer agents. The anti-cancer activity of [Co(phen)2(MeATSC)](NO3)3•1.5H2O•C2H5OH 1 (where phen = 1,10-phenanthroline and MeATSC = 9-anthraldehyde-N(4)-methylthiosemicarbazone) and [Cu(acetylethTSC)Cl]Cl•0.25C2H5OH 2 (where acetylethTSC = (E)-N-ethyl-2-[1-(thiazol-2-yl)ethylidene]hydrazinecarbothioamide) was investigated by analyzing DNA cleavage activity. The cytotoxic effect was analyzed using CCK-8 viability assay. The activities of caspase 3/7, 9, and 1, reactive oxygen species (ROS) production, cell cycle arrest, and mitochondrial function were further analyzed to study the cell death mechanisms. Complex 2 induced a significant increase in nicked DNA. The IC50 values of complex 1 were 17.59 μM and 61.26 μM in cancer and non-cancer cells, respectively. The IC50 values of complex 2 were 5.63 and 12.19 μM for cancer and non-cancer cells, respectively. Complex 1 induced an increase in ROS levels, mitochondrial dysfunction, and activated caspases 3/7, 9, and 1, which indicated the induction of intrinsic apoptotic pathway and pyroptosis. Complex 2 induced cell cycle arrest in the S phase, ROS generation, and caspase 3/7 activation. Thus, complex 1 induced cell death in the breast cancer cell line via activation of oxidative stress which induced apoptosis and pyroptosis while complex 2 induced cell cycle arrest through the induction of DNA cleavage.
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Affiliation(s)
- Duaa R. Alajroush
- Department of Chemistry and Biochemistry, Old Dominion University 4501 Elkhorn Avenue, Norfolk, VA 23529, U.S.A
| | - Chloe B. Smith
- Department of Chemistry and Biochemistry, Old Dominion University 4501 Elkhorn Avenue, Norfolk, VA 23529, U.S.A
| | - Brittney F. Anderson
- Department of Biological Sciences, University of the Virgin Islands, 2 John Brewers Bay, St. Thomas, VI 00802, U.S.A
| | - Ifeoluwa T. Oyeyemi
- Department of Chemistry and Biochemistry, Old Dominion University 4501 Elkhorn Avenue, Norfolk, VA 23529, U.S.A
- Department of Biological Sciences, University of Medical Sciences, Ondo City, Nigeria
| | - Stephen J. Beebe
- Frank Reidy Research center for Bioelectrics, Old Dominion University, 4211 Monarch Way, Suite 300, Norfolk, VA, 23508, U.S.A
| | - Alvin A. Holder
- Department of Chemistry and Biochemistry, Old Dominion University 4501 Elkhorn Avenue, Norfolk, VA 23529, U.S.A
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Oksuzoglu E, Yilmaz S, Yenice Cakmak G, Ataei S, Yildiz I. Antitumor activity against human promyelocytic leukemia and in silico studies of some benzoxazines. J Biomol Struct Dyn 2023; 41:8175-8190. [PMID: 36300440 DOI: 10.1080/07391102.2022.2130989] [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: 07/26/2022] [Accepted: 09/24/2022] [Indexed: 10/31/2022]
Abstract
Cancer is one of the deadliest diseases in the world today, and the incidence of cancer is increasing. Leukemia is a type of blood cancer defined as the uncontrolled proliferation of abnormal leukocytes in the blood and bone marrow. The HL-60 (human promyelocytic leukemia) cell line, derived from a single patient with acute promyelocytic leukemia, provides a unique in vitro model system for studying the cellular and molecular events involved in the proliferation and differentiation of leukemic cells. In this study, antitumor activities on the HL-60 of some of the resynthesized benzoxazine derivatives (BXN-01 and BXN-02) were investigated. The results of in vitro studies obtained were compared a standard drug, etoposide. In vitro results showed that BXN-01 and BXN-02 were found to be extremely effective compared to etoposide (IC50 value: 10 µM) with IC50 values of 5 nM and 25 nM, respectively. Furthermore, molecular docking studies were carried out for preliminary prediction of possible interaction modes between compounds and the active site of the target macromolecules, hTopo IIα, HDAC2, and RXRA. Then, in silico ADME/Tox studies were performed to predict drug-likeness and pharmacokinetic properties of BXN-01 and BXN-02.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Emine Oksuzoglu
- Molecular Biology Division, Department of Biology, Faculty of Science and Letters, Aksaray University, Aksaray, Turkey
| | - Serap Yilmaz
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Trakya University, Edirne, Turkey
| | - Gozde Yenice Cakmak
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Trakya University, Edirne, Turkey
- Graduate School of Health Sciences, Ankara University, Ankara, Turkey
| | - Sanaz Ataei
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
| | - Ilkay Yildiz
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
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Krochtová K, Halečková A, Janovec L, Blizniaková M, Kušnírová K, Kožurková M. Novel 3,9-Disubstituted Acridines with Strong Inhibition Activity against Topoisomerase I: Synthesis, Biological Evaluation and Molecular Docking Study. Molecules 2023; 28:1308. [PMID: 36770975 PMCID: PMC9921529 DOI: 10.3390/molecules28031308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
A series of novel 3,9-disubstituted acridines were synthesized and their biological potential was investigated. The synthetic plan consists of eight reaction steps, which produce the final products, derivatives 17a-17j, in a moderate yield. The principles of cheminformatics and computational chemistry were applied in order to study the relationship between the physicochemical properties of the 3,9-disubstituted acridines and their biological activity at a cellular and molecular level. The selected 3,9-disubstituted acridine derivatives were studied in the presence of DNA using spectroscopic (UV-Vis, circular dichroism, and thermal denaturation) and electrophoretic (nuclease activity, relaxation and unwinding assays for topoisomerase I and decatenation assay for topoisomerase IIα) methods. Binding constants (2.81-9.03 × 104 M-1) were calculated for the derivatives from the results of the absorption titration spectra. The derivatives were found to have caused the inhibition of both topoisomerase I and topoisomerase IIα. Molecular docking simulations suggested a different way in which the acridines 17a-17j can interact with topoisomerase I versus topoisomerase IIα. A strong correlation between the lipophilicity of the derivatives and their ability to stabilize the intercalation complex was identified for all of the studied agents. Acridines 17a-17j were also subjected to in vitro screening conducted by the Developmental Therapeutic Program of the National Cancer Institute (NCI) against a panel of 60 cancer cell lines. The strongest biological activity was displayed by aniline acridine 17a (MCF7-GI50 18.6 nM) and N,N-dimethylaniline acridine 17b (SR-GI50 38.0 nM). The relationship between the cytostatic activity of the most active substances (derivatives 17a, 17b, and 17e-17h) and their values of KB, LogP, ΔS°, and δ was also investigated. Due to the fact that a significant correlation was only found in the case of charge density, δ, it is possible to assume that the cytostatic effect might be dependent upon the structural specificity of the acridine derivatives.
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Affiliation(s)
- Kristína Krochtová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Annamária Halečková
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Ladislav Janovec
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Michaela Blizniaková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Katarína Kušnírová
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Mária Kožurková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
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Synthesis and Evaluation of Antiproliferative Activity, Topoisomerase IIα Inhibition, DNA Binding and Non-Clinical Toxicity of New Acridine-Thiosemicarbazone Derivatives. Pharmaceuticals (Basel) 2022; 15:ph15091098. [PMID: 36145320 PMCID: PMC9506480 DOI: 10.3390/ph15091098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we report the synthesis of twenty new acridine–thiosemicarbazone derivatives and their antiproliferative activities. Mechanisms of action such as the inhibition of topoisomerase IIα and the interaction with DNA have been studied for some of the most active derivatives by means of both in silico and in vitro methods, and evaluations of the non-clinical toxicities (in vivo) in mice. In general, the compounds showed greater cytotoxicity against B16-F10 cells, with the highest potency for DL-08 (IC50 = 14.79 µM). Derivatives DL-01 (77%), DL-07 (74%) and DL-08 (79%) showed interesting inhibition of topoisomerase IIα when compared to amsacrine, at 100 µM. In silico studies proposed the way of bonding of these compounds and a possible stereoelectronic reason for the absence of enzymatic activity for CL-07 and DL-06. Interactions with DNA presented different spectroscopic effects and indicate that the compound CL-07 has higher affinity for DNA (Kb = 4.75 × 104 M−1; Ksv = 2.6 × 103 M−1). In addition, compounds selected for non-clinical toxicity testing did not show serious signs of toxicity at the dose of 2000 mg/kg in mice; cytotoxic tests performed on leukemic cells (K-562) and its resistant form (K-562 Lucena 1) identified moderate potency for DL-01 and DL-08, with IC50 between 11.45 and 17.32 µM.
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Wu K, Peng X, Chen M, Li Y, Tang G, Peng J, Peng Y, Cao X. Recent progress of research on anti‐tumor agents using benzimidazole as the structure unit. Chem Biol Drug Des 2022; 99:736-757. [DOI: 10.1111/cbdd.14022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Kaiyue Wu
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Miaojia Chen
- Department of Pharmacy the first People's Hospital Pingjiang Yueyang Hunan China
| | - Yang Li
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering East China Jiaotong University Nanchang 330000 China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study College of Pharmacy Hengyang Medical School University of South China Hengyang China
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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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Ayyamperumal S, DJ D, Tallapaneni V, Mohan S, S B, Selvaraj J, Joghee NM, MJN C. Molecular docking analysis of α-Topoisomerase II with δ-Carboline derivatives as potential anticancer agents. Bioinformation 2021; 17:249-265. [PMID: 34393444 PMCID: PMC8340707 DOI: 10.6026/97320630017249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 11/29/2022] Open
Abstract
The enzyme, α-topoisomerase II (α-Topo II), is known to regulate efficiently the topology of DNA. It is highly expressed in rapidly proliferating cells and plays an important role in replication, transcription and chromosome organisation. This has prompted several investigators to pursue α-Topo II inhibitors as anticancer agents. δ-Carboline, a natural product, and its synthetic derivatives are known to exert potent anticancer activity by selectively targeting α-Topo II. Therefore, it is of interest to design carboline derivatives fused with pyrrolidine-2,5-dione in this context. δ-Carbolines fused with pyrrolidine-2,5-dione are of interest because the succinimide part of fused heteroaromatic molecule can interact with the ATP binding pocket via the hydrogen bond network with selectivity towards α-Topo II. The 300 derivatives designed were subjected to the Lipinski rule of 5, ADMET and toxicity prediction. The designed compounds were further analysed using molecular docking analysis on the active sites of the α-Topo II crystal structure (PDB ID:1ZXM). Molecular dynamic simulations were also performed to compare the binding mode and stability of the protein-ligand complexes. Compounds with ID numbers AS89, AS104, AS119, AS209, AS239, AS269, and AS299 show good binding activity compared to the co-crystal ligand. Molecular Dynamics simulation studies show that the ligand binding to α-Topo II in the ATP domain is stableand the protein-ligand conformation remains unchanged. Binding free energy calculations suggest that seven molecules designed are potential inhibitors for α-Topo II for further consideration as anticancer agents.
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Affiliation(s)
- Selvaraj Ayyamperumal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris - 643001,Tamil Nadu, India
| | - Dhananjay DJ
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi - 110067, India
| | - Vyshnavi Tallapaneni
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris - 643001,Tamil Nadu, India
| | - Surender Mohan
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi - 110067, India
| | - Basappa S
- Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore - 570006, Karnataka, India
| | - Jubie Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris - 643001,Tamil Nadu, India
| | - Nanjan Moola Joghee
- PG Studies and Research, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris - 643001, Tamil Nadu, India
| | - Chandrasekar MJN
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris - 643001,Tamil Nadu, India
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Buzun K, Bielawska A, Bielawski K, Gornowicz A. DNA topoisomerases as molecular targets for anticancer drugs. J Enzyme Inhib Med Chem 2020; 35:1781-1799. [PMID: 32975138 PMCID: PMC7534307 DOI: 10.1080/14756366.2020.1821676] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
The significant role of topoisomerases in the control of DNA chain topology has been confirmed in numerous research conducted worldwide. The prevalence of these enzymes, as well as the key importance of topoisomerase in the proper functioning of cells, have made them the target of many scientific studies conducted all over the world. This article is a comprehensive review of knowledge about topoisomerases and their inhibitors collected over the years. Studies on the structure-activity relationship and molecular docking are one of the key elements driving drug development. In addition to information on molecular targets, this article contains details on the structure-activity relationship of described classes of compounds. Moreover, the work also includes details about the structure of the compounds that drive the mode of action of topoisomerase inhibitors. Finally, selected topoisomerases inhibitors at the stage of clinical trials and their potential application in the chemotherapy of various cancers are described.
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Affiliation(s)
- Kamila Buzun
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Bialystok, Poland
| | - Agnieszka Gornowicz
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
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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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Shakya B, Yadav PN. Thiosemicarbazones as Potent Anticancer Agents and their Modes of Action. Mini Rev Med Chem 2020; 20:638-661. [DOI: 10.2174/1389557519666191029130310] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/17/2019] [Accepted: 10/03/2019] [Indexed: 11/22/2022]
Abstract
:Thiosemicarbazones (TSCs) are a class of Schiff bases usually obtained by the condensation of thiosemicarbazide with a suitable aldehyde or ketone. TSCs have been the focus of chemists and biologists due to their wide range of pharmacological effects. One of the promising areas in which these excellent metal chelators are being developed is their use against cancer. TSCs have a wide clinical antitumor spectrum with efficacy in various tumor types such as leukemia, pancreatic cancer, breast cancer, non-small cell lung cancer, cervical cancer, prostate cancer and bladder cancer. To obtain better activity, different series of TSCs have been developed by modifying the heteroaromatic system in their molecules. These compounds possessed significant antineoplastic activity when the carbonyl attachment of the side chain was located at a position α to the ring nitrogen atom, whereas attachment of the side chain β or γ to the heterocyclic N atom resulted in inactive antitumor agents. In addition, replacement of the heterocyclic ring N with C also resulted in a biologically inactive compound suggesting that a conjugated N,N,S-tridentate donor set is essential for the biological activities of thiosemicarbazones. Several possible mechanisms have been implemented for the anticancer activity of thiosemicarbazones.
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Affiliation(s)
- Bhushan Shakya
- Amrit Campus, Tribhuvan University, Thamel, Kathmandu, Nepal
| | - Paras Nath Yadav
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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Jamal QMS. Structural Recognition and Binding Pattern Analysis of Human Topoisomerase II Alpha with Steroidal Drugs: In Silico Study to Switchover the Cancer Treatment. Asian Pac J Cancer Prev 2020; 21:1349-1355. [PMID: 32458643 PMCID: PMC7541882 DOI: 10.31557/apjcp.2020.21.5.1349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/30/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Topoisomerase TOP-IIA (TTOP-IIA) is widely used as a significant target for cancer therapeutics because of its involvement in cell proliferation. Steroidal drugs have been suggested for breast cancer treatment as aromatase enzymes inhibitors . TTOP-IIA inhibitors can be used as a target for the development of new cancer therapeutics. MATERIALS AND METHODS In this study, we conducted a docking study on steroidal drugs Anastrozole (ANA), Letrozole (LET), and exemestane (EXE) with TTOP-IIA to explore the therapeutic area of these drugs. RESULTS The binding interaction of EXE drug had significant docking interaction which is followed by ANA and LET. Thus, all these drugs could be used to inhibit the TTOP-IIA mediated cell proliferation and could be a hope to treat the other types of cancers. Among all three tested steroidal drugs, EXE showed binding energy -7.05 kcal/mol, hydrogen bond length1.78289 Å and amino acid involved in an interaction was A: LYS723:HZ3 -: UNK1:O6. CONCLUSION The obtained data showed the most significant binding interaction analyzed with the tested enzyme. Thus, in vitro laboratory experimentation and in vivo research are necessary to put forward therapeutic repositioning of these drugs to establish them as a broad spectrum potential anticancer drugs. .
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Saudi Arabia.
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13
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Kadayat TM, Park S, Shrestha A, Jo H, Hwang SY, Katila P, Shrestha R, Nepal MR, Noh K, Kim SK, Koh WS, Kim KS, Jeon YH, Jeong TC, Kwon Y, Lee ES. Discovery and Biological Evaluations of Halogenated 2,4-Diphenyl Indeno[1,2- b]pyridinol Derivatives as Potent Topoisomerase IIα-Targeted Chemotherapeutic Agents for Breast Cancer. J Med Chem 2019; 62:8194-8234. [PMID: 31398033 DOI: 10.1021/acs.jmedchem.9b00970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the aim of developing new effective topoisomerase IIα-targeted anticancer agents, we synthesized a series of hydroxy- and halogenated 2,4-diphenyl indeno[1,2-b]pyridinols using a microwave-assisted single step synthetic method and investigated structure-activity relationships. The majority of compounds with chlorophenyl group at 2-position and phenol group at the 4-position of indeno[1,2-b]pyridinols exhibited potent antiproliferative activity and topoisomerase IIα-selective inhibition. Of the 172 compounds tested, 89 showed highly potent and selective topoisomerase IIα inhibition and antiproliferative activity in the nanomolar range against human T47D breast (2.6 nM) cancer cell lines. In addition, mechanistic studies revealed compound 89 is a nonintercalative topoisomerase II poison, and in vitro studies showed it had promising cytotoxic effects in diverse breast cancer cell lines and was particularly effective at inducing apoptosis in T47D cells. Furthermore, in vivo administration of compound 89 had significant antitumor effects in orthotopic mouse model of breast cancer.
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Affiliation(s)
- Tara Man Kadayat
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
- New Drug Development Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , Republic of Korea
| | - Seojeong Park
- College of Pharmacy, Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 120-750 , Republic of Korea
| | - Aarajana Shrestha
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Hyunji Jo
- College of Pharmacy, Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 120-750 , Republic of Korea
| | - Soo-Yeon Hwang
- College of Pharmacy, Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 120-750 , Republic of Korea
| | - Pramila Katila
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Ritina Shrestha
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Mahesh Raj Nepal
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Keumhan Noh
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Sang Kyoon Kim
- Laboratory Animal Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , Republic of Korea
| | - Woo-Suk Koh
- Laboratory Animal Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , Republic of Korea
| | - Kil Soo Kim
- Laboratory Animal Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , Republic of Korea
- College of Veterinary Medicine , Kyungpook National University , Daegu 41566 , Republic of Korea
| | - Yong Hyun Jeon
- Laboratory Animal Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , Republic of Korea
| | - Tae Cheon Jeong
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 120-750 , Republic of Korea
| | - Eung-Seok Lee
- College of Pharmacy , Yeungnam University , Gyeongsan 38541 , Republic of Korea
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14
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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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15
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Slater O, Kontoyianni M. The compromise of virtual screening and its impact on drug discovery. Expert Opin Drug Discov 2019; 14:619-637. [PMID: 31025886 DOI: 10.1080/17460441.2019.1604677] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Docking and structure-based virtual screening (VS) have been standard approaches in structure-based design for over two decades. However, our understanding of the limitations, potential, and strength of these techniques has enhanced, raising expectations. Areas covered: Based on a survey of reports in the past five years, we assess whether VS: (1) predicts binding poses in agreement with crystallographic data (when available); (2) is a superior screening tool, as often claimed; (3) is successful in identifying chemical scaffolds that can be starting points for subsequent lead optimization cycles. Data shows that knowledge of the target and its chemotypes in postprocessing lead to viable hits in early drug discovery endeavors. Expert opinion: VS is capable of accurate placements in the pocket for the most part, but does not consistently score screening collections accurately. What matters is capitalization on available resources to get closer to a viable lead or optimizable series. Integration of approaches, subjective hit selection guided by knowledge of the receptor or endogenous ligand, libraries driven by experimental guides, validation studies to identify the best docking/scoring that reproduces experimental findings, constraints regarding receptor-ligand interactions, thoroughly designed methodologies, and predefined cutoff scoring criteria strengthen VS's position in pharmaceutical research.
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Affiliation(s)
- Olivia Slater
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
| | - Maria Kontoyianni
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
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16
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Gahtori A, Singh A. Ligand-based Pharmacophore Model for Generation of Active Antidepressant- like Agents from Substituted 1,3,5 Triazine Class. Curr Comput Aided Drug Des 2018; 16:167-175. [PMID: 30569874 DOI: 10.2174/1573409915666181219125415] [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: 05/31/2018] [Revised: 11/06/2018] [Accepted: 12/16/2018] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Although the transition of a lead candidate into a drug is currently structured by well-defined milestone, it is still most challenging and offers no guarantee in success to the end. In fact, ligand-based pharmacophore modeling has become a key motive force for retrieving potential leads across several therapeutic areas. METHODS An urgent need towards the development of novel antidepressant agents led us to generate a pharmacophore model from an existing 44 compounds dataset. The best model with one hydrophobic, two ring aromatic, and one positive ionization features was chosen on behalf of the correlation coefficient, sensitivity, specificity, yield of actives and accuracy measures using HypoGen module of Discovery Studio. In house library consisting of 10,000 substituted 1,3,5 triazine derivatives were shortlisted to select four insilico hits. All shortlisted compounds were synthesized and characterized by FTIR, 1H-& 13C-NMR spectroscopy and finally tested for antidepressant-like activity using behavioral models on rats viz. Forced Swim Test (FST) and Elevated Plus Maze (EPM). RESULTS Two shortlisted compounds with optimal fit values showed a significant decrease in the duration of immobility as compared to standard drug Imipramine in FST while time spent in open arm in enhanced in case of EPM.
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Affiliation(s)
- Archana Gahtori
- Shri Guru Ram Rai Institute of Technology & Science, SGRR University, Patel Nagar Dehradun - 248001, Uttarakhand, India
| | - Abhishek Singh
- Shri Guru Ram Rai Institute of Technology & Science, SGRR University, Patel Nagar Dehradun - 248001, Uttarakhand, India
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17
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Shrestha A, Park S, Shin S, Man Kadayat T, Bist G, Katila P, Kwon Y, Lee ES. Design, synthesis, biological evaluation, structure-activity relationship study, and mode of action of 2-phenol-4,6-dichlorophenyl-pyridines. Bioorg Chem 2018; 79:1-18. [DOI: 10.1016/j.bioorg.2018.03.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/21/2018] [Accepted: 03/31/2018] [Indexed: 01/03/2023]
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18
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Mahalapbutr P, Chusuth P, Kungwan N, Chavasiri W, Wolschann P, Rungrotmongkol T. Molecular recognition of naphthoquinone-containing compounds against human DNA topoisomerase IIα ATPase domain: A molecular modeling study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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de Almeida SMV, Ribeiro AG, de Lima Silva GC, Ferreira Alves JE, Beltrão EIC, de Oliveira JF, de Carvalho LB, Alves de Lima MDC. DNA binding and Topoisomerase inhibition: How can these mechanisms be explored to design more specific anticancer agents? Biomed Pharmacother 2017; 96:1538-1556. [DOI: 10.1016/j.biopha.2017.11.054] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022] Open
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20
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Template selection and refinement considerations for modelling aminergic GPCR-ligand complexes. J Mol Graph Model 2017; 76:488-503. [PMID: 28818718 DOI: 10.1016/j.jmgm.2017.07.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are important targets for development of drugs for the treatment of many diseases. However, crystal structures are available for only a small fraction of these membrane bound proteins. Accurate homology models will provide opportunities for effective drug design targeting GPCRs. Recently, several serotonin receptor crystal structures were solved and needed to be evaluated as potential templates. In the first part of this work different measures of similarity in template selection were explored and methods for homology modelling, docking and refinement of aminergic GPCR-ligand complexes were developed and evaluated by comparing models of the D3-R/eticlopride complex with the crystal structure. Homology models of the three α1 adrenergic receptor subtypes and of a serotonin receptor subtype were then constructed using these methods These models were evaluated by docking a range of antagonists into them.
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21
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Dobiaš J, Ondruš M, Addová G, Boháč A. Switchable highly regioselective synthesis of 3,4-dihydroquinoxalin-2(1 H)ones from o-phenylenediamines and aroylpyruvates. Beilstein J Org Chem 2017; 13:1350-1360. [PMID: 28781701 PMCID: PMC5530724 DOI: 10.3762/bjoc.13.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/21/2017] [Indexed: 01/14/2023] Open
Abstract
3-Acylmethylidene-3,4-dihydroquinoxalin-2(1H)-ones are compounds which possess a wide range of physical and pharmaceutical applications. These compounds can be easily prepared by cyclocondensation of o-phenylenediamines and aroylpyruvates. Unsymmetrically substituted o-phenylenediamines can be obtained form regioisomeric mixtures of 3,4-dihydroquinoxalin-2(1H)-ones. It is often quite difficult to get a pure regioisomer and determine its structure without controlling the reaction selectivity and exploitation of complex NMR techniques (HSQC, NOESY, HMBC). This article examines the regioselectivity of the cyclocondensation between six monosubstituted o-phenylenediamines (-OMe, -F, -Cl, -COOH, -CN, -NO2) and the derivatives of p-chlorobenzoylpyruvate (ester or acid) which we studied. Six regioisomeric 3,4-dihydroquinoxalin-2(1H)-one pairs were selectively prepared and characterised. Based on our experiences, a simplified methodology for determining the structure of the regioisomers was proposed. We developed two general and highly selective methodologies starting from the same o-phenylenediamines and activated 4-chlorobenzoylpyruvates (ester or acid) enabling switching of 3,4-dihydroquinoxalin-2(1H)-one regioselectivity in a predictable manner. For comparison, all regioselective cyclocondensations were performed with the same standardized conditions (DMF, rt, 3 days), differing only by the additives p-TsOH or HOBt/DIC (hydroxybenzotriazole/N,N'-diisopropylcarbodiimide). Both selected methods are simple, general and highly regioselective (72-97%). A mechanism for the regioselectivity was also proposed and discussed. This study can be used as a guide when choosing the most optimal reaction conditions for the synthesis of the desired 3,4-dihydroquinoxalin-2(1H)-one regioisomers with the best selectivity. The demonstrated methodologies in this article may also be applied to differently substituted 3,4-dihydroquinoxalin-2(1H)-ones in general, which could expand the synthetic impact of our results.
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Affiliation(s)
- Juraj Dobiaš
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Marek Ondruš
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Gabriela Addová
- Institute of Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Andrej Boháč
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Biomagi, Ltd., Mamateyova 26, 851 04 Bratislava, Slovakia
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22
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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23
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Structural basis of DNA topoisomerase II-α (Top2-α) inhibition: a computational analysis of interactions between Top2-α and its inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1567-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Ahmadi M, Nowroozi A, Shahlaei M. Constructing an atomic-resolution model of human P2X7 receptor followed by pharmacophore modeling to identify potential inhibitors. J Mol Graph Model 2015; 61:243-61. [PMID: 26298810 DOI: 10.1016/j.jmgm.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/22/2022]
Abstract
The P2X purinoceptor 7 (P2X7R) is a trimeric ATP-activated ion channel gated by extracellular ATP. P2X7R has important role in numerous diseases including pain, neurodegeneration, and inflammatory diseases such as rheumatoid arthritis and osteoarthritis. In this prospective, the discovery of small-molecule inhibitors for P2X7R as a novel therapeutic target has received considerable attention in recent years. At first, 3D structure of P2X7R was built by using homology modeling (HM) and a 50ns molecular dynamics simulation (MDS). Ligand-based quantitative pharmacophore modeling methodology of P2X7R antagonists were developed based on training set of 49 compounds. The best four-feature pharmacophore model, includes two hydrophobic aromatic, one hydrophobic and one aromatic ring features, has the highest correlation coefficient (0.874), cost difference (368.677), low RMSD (2.876), as well as it shows a high goodness of fit and enrichment factor. Consequently, some hit compounds were introduced as final candidates by employing virtual screening and molecular docking procedure simultaneously. Among these compounds, six potential molecule were identified as potential virtual leads which, as such or upon further optimization, can be used to design novel P2X7R inhibitors.
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Affiliation(s)
- Mehdi Ahmadi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Nowroozi
- Pharmaceutical sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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25
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Palermo G, Minniti E, Greco ML, Riccardi L, Simoni E, Convertino M, Marchetti C, Rosini M, Sissi C, Minarini A, De Vivo M. An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512. Chem Commun (Camb) 2015; 51:14310-3. [PMID: 26234198 DOI: 10.1039/c5cc05065k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combined computational-experimental analyses explain and quantify the spermine-vectorized F14512's boosted potency as a topoII poison. We found that an optimized polyamine moiety boosts drug binding to the topoII/DNA cleavage complex, rather than to the DNA alone. These results provide new structural bases and key reference data for designing new human topoII poisons.
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Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
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