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Pal S, Paul B, Bandopadhyay P, Preethy N, Sarkar D, Rahaman O, Goon S, Roy S, Ganguly D, Talukdar A. Synthesis and characterization of new potent TLR7 antagonists based on analysis of the binding mode using biomolecular simulations. Eur J Med Chem 2020; 210:112978. [PMID: 33189437 DOI: 10.1016/j.ejmech.2020.112978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Aberrant activation of the endosomal Toll-like receptor 7 (TLR7) has been implicated in myriad autoimmune diseases and is an established therapeutic target in such conditions. Development of diverse TLR7 antagonists is mainly accomplished through random screening. To correlate human TLR7 (hTLR7) antagonistic activity with the structural features in different chemotypes, we derived a hypothetical binding model based on molecular docking analysis along with molecular dynamics (MD) simulations study. The binding hypothesis revealed different pockets, grooves and a central cavity where ligand-receptor interaction with specific residues through hydrophobic and hydrogen bond interactions take place, which correlate with TLR7 antagonistic activity thus paving the way for rational design using varied chemotypes. Based on the structural insight thus gained, TLR7 antagonists with quinazoline were designed to understand the effect of engagement of these pockets as well as boundaries of the chemical space associated with them. The newly synthesized most potent hTLR7 antagonist, i.e. compound 63, showed IC50 value of 1.03 ± 0.05 μM and was validated by performing primary assay in human plasmacytoid dendritic cells (pDC) (IC50pDC: 1.42 μM). The biological validation of the synthesized molecules was performed in TLR7-reporter HEK293 cells as well as in human plasmacytoid dendritic cells (pDCs). Our study provides a rational design approach thus facilitating further development of novel small molecule hTLR7 antagonists based on different chemical scaffolds.
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Affiliation(s)
- Sourav Pal
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Barnali Paul
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Purbita Bandopadhyay
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata, 700091, WB, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Nagothy Preethy
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Oindrila Rahaman
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata, 700091, WB, India
| | - Sunny Goon
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Swarnali Roy
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata, 700091, WB, India
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India.
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2
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Azimi F, Ghasemi JB, Saghaei L, Hassanzadeh F, Mahdavi M, Sadeghi-Aliabadi H, Scotti MT, Scotti L. Identification of Essential 2D and 3D Chemical Features for Discovery of the Novel Tubulin Polymerization Inhibitors. Curr Top Med Chem 2019; 19:1092-1120. [DOI: 10.2174/1568026619666190520083655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/12/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022]
Abstract
Background:
Tubulin polymerization inhibitors interfere with microtubule assembly and
their functions lead to mitotic arrest, therefore they are attractive target for design and development of
novel anticancer compounds.
Objective:
The proposed novel and effective structures following the use of three-dimensionalquantitative
structure activity relationship (3D-QSAR) pharmacophore based virtual screening clearly
demonstrate the high efficiency of this method in modern drug discovery.
Method:
Combined computational approach was applied to extract the essential 2D and 3D features
requirements for higher activity as well as identify new anti-tubulin agents.
Results:
The best quantitative pharmacophore model, Hypo1, exhibited good correlation of 0.943
(RMSD=1.019) and excellent predictive power in the training set compounds. Generated model
AHHHR, was well mapped to colchicine site and three-dimensional spatial arrangement of their features
were in good agreement with the vital interactions in the active site. Total prediction accuracy
(0.92 for training set and 0.86 for test set), enrichment factor (4.2 for training set and 4.5 for test set)
and the area under the ROC curve (0.86 for training set and 0.94 for the test set), the developed model
using Extended Class FingerPrints of maximum diameter 4 (ECFP_4) was chosen as the best model.
Conclusion:
Developed computational platform provided a better understanding of requirement features
for colchicine site inhibitors and we believe the results of this study might be useful for the rational
design and optimization of new inhibitors.
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Affiliation(s)
- Fateme Azimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jahan B. Ghasemi
- Department of Chemistry, Faculty of Sciences, University of Tehran, Tehran, Iran
| | - Lotfollah Saghaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farshid Hassanzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marcus T. Scotti
- Federal University of Paraiba, Health Sciences Center, Campus I, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Federal University of Paraiba, Health Sciences Center, Campus I, Joao Pessoa, PB, Brazil
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3
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Ali EMH, Abdel-Maksoud MS, Oh CH. Thieno[2,3-d]pyrimidine as a promising scaffold in medicinal chemistry: Recent advances. Bioorg Med Chem 2019; 27:1159-1194. [PMID: 30826188 DOI: 10.1016/j.bmc.2019.02.044] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/16/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022]
Abstract
Thienopyrimidine scaffold is a fused heterocyclic ring system that structurally can be considered as adenine, the purine base that is found in both DNA and RNA-bioisosteres. Thienopyrimidines exist in three distinct isomeric forms. The current review discusses thieno[2,3-d]pyrimidine as a one of the opulent heterocycles in drug discovery. Its broad range of medical applications such as anticancer, anti-inflammatory, anti-microbial, and CNS protective agents has inspired us to study its structure-activity relationship (SAR), along with its relevant synthetic strategies. The present review briefly summarizes synthetic approaches for the preparation of thieno[2,3-d]pyrimidine derivatives. In addition, the promising biological activities of this scaffold are also illustrated with explanatory diagrams for their SAR studies.
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Affiliation(s)
- Eslam M H Ali
- Center for Biomaterials, Korea Institute of Science & Technology (KIST), Seoul, Seongbuk-gu 02792, Republic of Korea; Department of Biomolecular Science, University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea
| | - Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (NRC), Dokki, Giza 12622, Egypt
| | - Chang-Hyun Oh
- Center for Biomaterials, Korea Institute of Science & Technology (KIST), Seoul, Seongbuk-gu 02792, Republic of Korea; Department of Biomolecular Science, University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea.
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4
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Damale MG, Patil RB, Ansari SA, Alkahtani HM, Almehizia AA, Shinde DB, Arote R, Sangshetti J. Molecular docking, pharmacophore based virtual screening and molecular dynamics studies towards the identification of potential leads for the management of H. pylori. RSC Adv 2019; 9:26176-26208. [PMID: 35531003 PMCID: PMC9070323 DOI: 10.1039/c9ra03281a] [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] [Received: 05/02/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
The enzyme pantothenate synthetase panC is one of the potential new antimicrobial drug targets, but it is poorly characterized in H. pylori. H. pylori infection can cause gastric cancer and the management of H. pylori infection is crucial in various gastric ulcers and gastric cancer. The current study describes the use of innovative drug discovery and design approaches like comparative metabolic pathway analysis (Metacyc), exploration of database of essential genes (DEG), homology modelling, pharmacophore based virtual screening, ADMET studies and molecular dynamics simulations in identifying potential lead compounds for the H. pylori specific panC. The top ranked virtual hits STOCK1N-60270, STOCK1N-63040, STOCK1N-44424 and STOCK1N-63231 can act as templates for synthesis of new H. pylori inhibitors and they hold a promise in the management of gastric cancers caused by H. pylori. Computational approaches such as pharmacophore modeling, virtual screening and MD simulations were explored to find the potential hits as H. pylori specific panC inhibitors for the management of gastric ulcers and gastric cancers.![]()
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Affiliation(s)
- Manoj G. Damale
- Department of Pharmaceutical Medicinal Chemistry
- Srinath College of Pharmacy
- Aurangabad
- India
| | - Rajesh B. Patil
- Sinhgad Technical Education Society's
- Smt. Kashibai Navale College of Pharmacy
- Pune
- India
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Abdulrahman A. Almehizia
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | | | - Rohidas Arote
- Department of Molecular Genetics
- School of Dentistry
- Seoul National University
- Seoul
- Republic of Korea
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Wang X, Lei B, Ma L, Jiao H, Xing W, Chen J, Li Z. Iron-catalyzed C(5)−H Imidation of Azole with N
-Fluorobenzenesulfonimide. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201701124] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaojiao Wang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Bowen Lei
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Lifang Ma
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Huixuan Jiao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Wenhua Xing
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Jiaming Chen
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
| | - Ziyuan Li
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering; Sichuan University; Chengdu 610065 People's Republic of China
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6
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Park CH, Lee C, Yang JS, Joe BY, Chun K, Kim H, Kim HY, Kang JS, Lee JI, Kim MH, Han G. Discovery of thienopyrimidine-based FLT3 inhibitors from the structural modification of known IKKβ inhibitors. Bioorg Med Chem Lett 2014; 24:2655-60. [DOI: 10.1016/j.bmcl.2014.04.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/15/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
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7
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Lu S, Sun SL, Liu HC, Chen YD, Yuan HL, Gao YP, Yang P, Lu T. Identification of novel polo-like kinase 1 inhibitors by a hybrid virtual screening. Chem Biol Drug Des 2012; 80:328-39. [PMID: 22583481 DOI: 10.1111/j.1747-0285.2012.01412.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Polo-like kinase 1 is an important and attractive oncological target that plays a key role in mitosis and cytokinesis. A combined pharmacophore- and docking-based virtual screening was performed to identify novel polo-like kinase 1 inhibitors. A total of 34 hit compounds were selected and tested in vitro, and some compounds showed inhibition of polo-like kinase 1 and human tumor cell growth. The most potent compound (66) inhibited polo-like kinase 1 with an IC(50) value of 6.99 μm. The docked binding models of two hit compounds were discussed in detail. These compounds contained novel chemical scaffolds and may be used as foundations for the development of novel classes of polo-like kinase 1 inhibitors.
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Affiliation(s)
- Shuai Lu
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
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8
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Zhang J, Lu M, Zhou F, Sun H, Hao G, Wu X, Wang G. Key role of nuclear factor-κB in the cellular pharmacokinetics of adriamycin in MCF-7/Adr cells: the potential mechanism for synergy with 20(S)-ginsenoside Rh2. Drug Metab Dispos 2012; 40:1900-8. [PMID: 22745335 DOI: 10.1124/dmd.112.045187] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have previously demonstrated that ginsenoside 20(S)-Rh2 is a potent ATP-binding cassette (ABC) B1 inhibitor and explored the cellular pharmacokinetic mechanisms for its synergistic effect on the cytotoxicity of adriamycin. The present studies were conducted to elucidate the key factors that influenced ABCB1 expression, which could further alter adriamycin cellular pharmacokinetics. Meanwhile, the influence of 20(S)-Rh2 on the above factors was revealed for explaining its synergistic effect from the view of ABCB1 expression. The results indicated that 20(S)-Rh2 inhibited adriamycin-induced ABCB1 expression in MCF-7/Adr cells. Subsequent analyses indicated that 20(S)-Rh2 markedly inhibited adriamycin-induced activation of the mitogen-activated protein kinase (MAPK)/nuclear factor (NF)-κB pathway, NF-κB translocation to the nucleus, and NF-κB binding activity. Furthermore, 20(S)-Rh2 repressed the Adriamycin-enhanced ability of NF-κB to bind to the human multidrug resistance (MDR1) promoter, and MAPK/NF-κB inhibitors and NF-κB small interfering RNA reversed the adriamycin-induced expression of ABCB1. Moreover, the cellular pharmacokinetics of adriamycin was also significantly altered by inhibiting NF-κB. In conclusion, the MAPK/NF-κB pathway mediates adriamycin-induced ABCB1 expression and subsequently alters the cellular pharmacokinetics of adriamycin. It was speculated that 20(S)-Rh2 acted on this pathway to lower adriamycin-induced ABCB1 expression in MCF-7/Adr cells, which provided mechanism-based support to the development of 20(S)-Rh2 as a MDR reversal agent.
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Affiliation(s)
- Jingwei Zhang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, Jiangsu, China
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9
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Chen Y, Fang L, Peng S, Liao H, Lehmann J, Zhang Y. Discovery of a novel acetylcholinesterase inhibitor by structure-based virtual screening techniques. Bioorg Med Chem Lett 2012; 22:3181-7. [DOI: 10.1016/j.bmcl.2012.03.046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/09/2012] [Accepted: 03/10/2012] [Indexed: 10/28/2022]
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10
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Sun H, Chen F, Wang X, Liu Z, Yang Q, Zhang X, Zhu J, Qiang L, Guo Q, You Q. Studies on gambogic acid (IV): Exploring structure-activity relationship with IκB kinase-beta (IKKβ). Eur J Med Chem 2012; 51:110-23. [PMID: 22472167 DOI: 10.1016/j.ejmech.2012.02.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 01/04/2023]
Abstract
Previously we have reported a series of gambogic acid's analogs and have identified a compound that possessed comparable in vitro growth inhibitory effect as gambogic acid. However, their target protein as well as the key pharmacophoric motifs on the target have not been identified yet. Herein we report that gambogic acid and its analogs inhibit the activity of IκB Kinase-beta (IKKβ) through suppressing the activation of TNFα/NF-κB pathway, which in turn induces A549 and U251 cell apoptosis. IKKβ can serve as one of gambogic acid's targets. The preparation of the compounds was carefully discussed in the article. Caged 4-oxa-tricyclo[4.3.1.0(3,7)]dec-2-one xanthone, which was identified as the pharmacophoric scaffold, represents a promising therapeutic agent for cancer and useful probe against NF-κB pathway.
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Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, China
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