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Salam R, Bakker M, Krutáková M, Štefela A, Pávek P, Duintjer Tebbens J, Zitko J. The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach. Arch Pharm (Weinheim) 2025; 358:e2400423. [PMID: 39801251 PMCID: PMC11726147 DOI: 10.1002/ardp.202400423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 12/11/2024] [Accepted: 12/19/2024] [Indexed: 01/16/2025]
Abstract
The Takeda G protein-coupled receptor 5 (TGR5), also known as GPBAR1 (G protein-coupled bile acid receptor), is a membrane-type bile acid receptor that regulates blood glucose levels and energy expenditure. These essential functions make TGR5 a promising target for the treatment of type 2 diabetes and metabolic disorders. Currently, most research on developing TGR5 agonists focuses on modifying the structure of bile acids, which are the endogenous ligands of TGR5. However, TGR5 agonists with nonsteroidal structures have not been widely explored. This study aimed at discovering new TGR5 agonists using bile acid derivatives as a basis for a computational approach. We applied a combination of pharmacophore-based, molecular docking, and molecular dynamic (MD) simulation to identify potential compounds as new TGR5 agonists. Through pharmacophore screening and molecular docking, we identified 41 candidate compounds. From these, five candidates were selected based on criteria including pharmacophore features, a docking score of less than 9.2 kcal/mol, and similarity in essential interaction patterns with a reference ligand. Biological assays of the five hits confirmed that Hit-3 activates TGR5 similarly to the bile acid control. This was supported by MD simulation results, which indicated that a hydrogen bond interaction with Tyr240 is involved in TGR5 activation. Hit-3 (CSC089939231) represents a new nonsteroidal lead that can be further optimized to design potent TGR5 agonists.
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Affiliation(s)
- Rudy Salam
- Department of Biophysics and Physical Chemistry, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
- Department of Pharmacy, Faculty of MedicineUniversitas BrawijayaMalangIndonesia
| | - Michael Bakker
- Department of Biophysics and Physical Chemistry, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
| | - Mária Krutáková
- Department of Pharmacology and Toxicology, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
| | - Alžbeta Štefela
- Department of Pharmacology and Toxicology, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
| | - Petr Pávek
- Department of Pharmacology and Toxicology, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
| | - Jurjen Duintjer Tebbens
- Department of Biophysics and Physical Chemistry, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
| | - Jan Zitko
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of PharmacyCharles UniversityHradec KrálovéCzech Republic
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Khatun S, Dasgupta I, Islam R, Amin SA, Jha T, Dhaked DK, Gayen S. Unveiling critical structural features for effective HDAC8 inhibition: a comprehensive study using quantitative read-across structure-activity relationship (q-RASAR) and pharmacophore modeling. Mol Divers 2024; 28:2197-2215. [PMID: 38871969 DOI: 10.1007/s11030-024-10903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Histone deacetylases constitute a group of enzymes that participate in several biological processes. Notably, inhibiting HDAC8 has become a therapeutic strategy for various diseases. The current inhibitors for HDAC8 lack selectivity and target multiple HDACs. Consequently, there is a growing recognition of the need for selective HDAC8 inhibitors to enhance the effectiveness of therapeutic interventions. In our current study, we have utilized a multi-faceted approach, including Quantitative Structure-Activity Relationship (QSAR) combined with Quantitative Read-Across Structure-Activity Relationship (q-RASAR) modeling, pharmacophore mapping, molecular docking, and molecular dynamics (MD) simulations. The developed q-RASAR model has a high statistical significance and predictive ability (Q2F1:0.778, Q2F2:0.775). The contributions of important descriptors are discussed in detail to gain insight into the crucial structural features in HDAC8 inhibition. The best pharmacophore hypothesis exhibits a high regression coefficient (0.969) and a low root mean square deviation (0.944), highlighting the importance of correctly orienting hydrogen bond acceptor (HBA), ring aromatic (RA), and zinc-binding group (ZBG) features in designing potent HDAC8 inhibitors. To confirm the results of q-RASAR and pharmacophore mapping, molecular docking analysis of the five potent compounds (44, 54, 82, 102, and 118) was performed to gain further insights into these structural features crucial for interaction with the HDAC8 enzyme. Lastly, MD simulation studies of the most active compound (54, mapped correctly with the pharmacophore hypothesis) and the least active compound (34, mapped poorly with the pharmacophore hypothesis) were carried out to validate the observations of the studies above. This study not only refines our understanding of essential structural features for HDAC8 inhibition but also provides a robust framework for the rational design of novel selective HDAC8 inhibitors which may offer insights to medicinal chemists and researchers engaged in the development of HDAC8-targeted therapeutics.
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Affiliation(s)
- Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Indrasis Dasgupta
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Rakibul Islam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, 700054, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Devendra Kumar Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, 700054, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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Zheng L, Zhang Y, Mei S, Xie T, Zou Y, Wang Y, Jing H, Xu S, Dramou P, Xu Z, Li J, Zhou Y, Niu MM. Discovery of a Potent Dual Son of Sevenless 1 (SOS1) and Epidermal Growth Factor Receptor (EGFR) Inhibitor for the Treatment of Prostate Cancer. J Med Chem 2024; 67:7130-7145. [PMID: 38630077 DOI: 10.1021/acs.jmedchem.3c02433] [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: 07/31/2024]
Abstract
Multitarget medications represent an appealing therapy against the disease with multifactorial abnormalities─cancer. Therefore, simultaneously targeting son of sevenless 1 (SOS1) and epidermal growth factor receptor (EGFR), two aberrantly expressed proteins crucial for the oncogenesis and progression of prostate cancer, may achieve active antitumor effects. Here, we discovered dual SOS1/EGFR-targeting compounds via pharmacophore-based docking screening. The most prominent compound SE-9 exhibited nanomolar inhibition activity against both SOS1 and EGFR and efficiently suppressed the phosphorylation of ERK and AKT in prostate cancer cells PC-3. Cellular assays also revealed that SE-9 displayed strong antiproliferative activities through diverse mechanisms, such as induction of cell apoptosis and G1 phase cell cycle arrest, as well as reduction of angiogenesis and migration. Further in vivo findings showed that SE-9 potently inhibited tumor growth in PC-3 xenografts without obvious toxicity. Overall, SE-9 is a novel dual-targeting SOS1/EGFR inhibitor that represents a promising treatment strategy for prostate cancer.
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Affiliation(s)
- Lufeng Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Yuxin Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
| | - Tianyuan Xie
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
| | - Yuting Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Han Jing
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Pierre Dramou
- Department of Analytical Chemistry, School of Sciences, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Xu
- Department of Pharmacy, Taizhou School of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Jindong Li
- Taizhou School of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Yang Zhou
- Department of Pathology, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
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Jana A, Naga R, Saha S, Griñán-Ferré C, Banerjee DR. Integration of ligand and structure-based pharmacophore screening for the identification of novel natural leads against Euchromatic histone lysine methyltransferase 2 (EHMT2/G9a). J Biomol Struct Dyn 2024; 42:3535-3562. [PMID: 37216299 DOI: 10.1080/07391102.2023.2213346] [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: 02/14/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023]
Abstract
Herein, we report a blended ligand and structure-based pharmacophore screening approach to identify new natural leads against the Protein Lysine Methyltransferase 2 (EHMT2/G9a). The EHMT2/G9a has been associated with Cancer, Alzheimer's, and aging and is considered an emerging drug target having no clinically passed inhibitor. Purposefully, we developed the ligand-based pharmacophore (Pharmacophore-L) based on the common features of known inhibitors and the structure-based pharmacophore (Pharmacophore-S) based on the interaction profile of available crystal structures. The Pharmacophore-L and Pharmacophore-S were subjected to multiple tiers of validations and utilized in combination for the screening of total 741543 compounds coming from multiple databases. Additional layers of stringency were applied in the screening process to test drug-likeness (using Lipinski's rule, Veber's rule, SMARTS and ADMET filtration), to rule out any toxicity (TOPKAT analysis). The interaction profiles, stabilities, and comparative analysis against the reference were carried out by flexible docking, MD simulation, and MM-GBSA analysis, which finally led to three leads as potential inhibitors of G9a.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhisek Jana
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
| | - Rahul Naga
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Deb Ranjan Banerjee
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
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Dubey P, Pathak DP, Ali F, Chauhan G, Kalaiselvan V. In-vitro Evaluation of Triazine Scaffold for Anticancer Drug Development: A Review. Curr Drug Discov Technol 2024; 21:e170723218813. [PMID: 37461340 DOI: 10.2174/1570163820666230717161610] [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: 09/16/2022] [Revised: 03/27/2023] [Accepted: 05/12/2023] [Indexed: 07/21/2023]
Abstract
INTRODUCTION The widespread importance of the synthesis and modification of anticancer agents has given rise to many numbers of medicinal chemistry programs. In this regard, triazine derivatives have attracted attention due to their remarkable activity against a wide range of cancer cells. This evaluation covers work reports to define the anticancer activity, the most active synthesized compound for the target, the SAR and, when described, the probable MOA besides similarly considered to deliver complete and target-pointed data for the development of types of anti-tumour medicines of triazine derivatives. Triazine scaffold for the development of anticancer analogues. Triazine can also relate to numerous beneficial targets, and their analogues have auspicious in-vitro and in-vivo anti-tumour activity. Fused molecules can improve efficacy, and drug resistance and diminish side effects, and numerous hybrid molecules are beneath diverse stages of clinical trials, so hybrid derivatives of triazine may offer valuable therapeutic involvement for the dealing of tumours. OBJECTIVE The objective of the recent review was to summarize the recent reports on triazine as well as its analogues with respect to its anticancer therapeutic potential. CONCLUSION The content of the review would be helpful to update the researchers working towards the synthesis and designing of new molecules for the treatment of various types of cancer disease with the recent molecules that have been produced from the triazine scaffold. Triazine scaffolds based on 1,3,5-triazine considerably boost molecular diversity levels and enable covering chemical space in key medicinal chemistry fields.
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Affiliation(s)
- Pragya Dubey
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli- Badarpur Road, Sector 3, Pushp Vihar, New Delhi, 110017, India
| | - Dharam Pal Pathak
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli- Badarpur Road, Sector 3, Pushp Vihar, New Delhi, 110017, India
| | - Faraat Ali
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, Hradec Králové 500 05, Czech Republic
- Department of Licensing and Enforcement, Laboratory Services, Botswana Medicines Regulatory Authority, Gaborone, Botswana
| | - Garima Chauhan
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, Mehrauli- Badarpur Road, Sector 3, Pushp Vihar, New Delhi, 110017, India
| | - Vivekanandan Kalaiselvan
- Indian Pharmacopoeia Commission, Ministry of Health and Family Welfare, Government of India, Sector-23, Raj Nagar, Ghaziabad 201002, India
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Mandour AA, Elkaeed EB, Hagras M, Refaat HM, Ismail NS. Virtual screening approach for the discovery of selective 5α-reductase type II inhibitors for benign prostatic hyperplasia treatment. Future Med Chem 2023; 15:2149-2163. [PMID: 37955117 DOI: 10.4155/fmc-2023-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Background: 5α-Reductase type II (5αR2) inhibition is a promising strategy for benign prostatic hyperplasia treatment. A computational approach including virtual screening, ligand-based 3D pharmacophore modeling, 2D quantitative structure-activity relationship and molecular docking simulations were adopted to develop novel inhibitors. Results: Hits were first filtered via the validated pharmacophore and 2D quantitative structure-activity relationship models. Docking on the recently determined cocrystallized structure of 5αR2 showed three promising hits. Visual inspection results were compared with finasteride ligand and dihydrotestosterone as reference, to explain the role of binding to Glu57 and Tyr91 for 5αR2 selective inhibition. Conclusion: Alignment between Hit 2 and finasteride in the binding pocket showed similar binding modes. The biological activity prediction showed antitumor and androgen targeting activity of the new hits.
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Affiliation(s)
- Asmaa A Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, 13713, Saudi Arabia
| | - Mohamed Hagras
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Hanan M Refaat
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
| | - Nasser Sm Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, 11835, Egypt
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Khadempar S, Lotfi M, Haghiralsadat F, Saidijam M, Ghasemi N, Afshar S. Lansoprazole as a potent HDAC2 inhibitor for treatment of colorectal cancer: An in-silico analysis and experimental validation. Comput Biol Med 2023; 166:107518. [PMID: 37806058 DOI: 10.1016/j.compbiomed.2023.107518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Histone deacetylase 2 (HDAC2), belonging to the class I HDAC family, holds significant therapeutic potential as a crucial target for diverse cancer types. As key players in the realm of epigenetic regulatory enzymes, histone deacetylases (HDACs) are intricately involved in the onset and progression of cancer. Consequently, pursuing isoform-specific inhibitors targeting histone deacetylases (HDACs) has garnered substantial interest in both biological and medical circles. The objective of the present investigation was to employ a drug repurposing approach to discover novel and potent HDAC2 inhibitors. MATERIALS AND METHODS In this study, our protocol is presented on virtual screening to identify novel potential HDAC2 inhibitors through 3D-QSAR, molecular docking, pharmacophore modeling, and molecular dynamics (MD) simulation. Afterward, In-vitro assays were employed to evaluate the cytotoxicity, apoptosis, and migration of HCT-116 cell lines under treatment of hit compound and valproic acid as a control inhibitor. The expression levels of HDAC2, TP53, BCL2, and BAX were evaluated by QRT-PCR. RESULTS RMSD, RMSF, H-bond, and DSSP analysis results confirmed that among bioinformatically selected compounds, lansoprazole exhibited the highest HDAC2 inhibitory potential. Experimental validation revealed that lansoprazole displayed significant antiproliferative activity. The determined IC50 value was 400 ± 2.36 μM. Furthermore, the apoptotic cells ratio concentration-dependently increased under Lansoprazole treatment. Results of the Scratch assay indicated that lansoprazole led to decreasing the migration of CRC cells. Finally, under Lansoprazole treatment the expression level of BCL2 and HDAC2 decreased and BAX and TP53 increased. CONCLUSION Taking together the results of the current study indicated that Lansoprazole as a novel HDAC2 inhibitor, could be used as a potential therapeutic agent for the treatment of CRC. Although, further experimental studies should be performed before using this compound in the clinic.
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Affiliation(s)
- Saedeh Khadempar
- Department of Medical Genetics, Shahid Sadoughi University of Medical Science, Yazd, Iran.
| | - Marzieh Lotfi
- Abortion Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran.
| | - Fatemeh Haghiralsadat
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Nasrin Ghasemi
- Abortion Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran.
| | - Saeid Afshar
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
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Vásquez AF, Gómez LA, González Barrios A, Riaño-Pachón DM. Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors. Int J Mol Sci 2022; 23:13946. [PMID: 36430425 PMCID: PMC9694616 DOI: 10.3390/ijms232213946] [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: 09/06/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Antifolates such as methotrexate (MTX) have been largely known as anticancer agents because of their role in blocking nucleic acid synthesis and cell proliferation. Their mechanism of action lies in their ability to inhibit enzymes involved in the folic acid cycle, especially human dihydrofolate reductase (hDHFR). However, most of them have a classical structure that has proven ineffective against melanoma, and, therefore, inhibitors with a non-classical lipophilic structure are increasingly becoming an attractive alternative to circumvent this clinical resistance. In this study, we conducted a protocol combining virtual screening (VS) and cell-based assays to identify new potential non-classical hDHFR inhibitors. Among 173 hit compounds identified (average logP = 3.68; average MW = 378.34 Da), two-herein, called C1 and C2-exhibited activity against melanoma cell lines B16 and A375 by MTT and Trypan-Blue assays. C1 showed cell growth arrest (39% and 56%) and C2 showed potent cytotoxic activity (77% and 51%) in a dose-dependent manner. The effects of C2 on A375 cell viability were greater than MTX (98% vs 60%) at equivalent concentrations and times. Our results indicate that the integrated in silico/in vitro approach provided a benchmark to identify novel promising non-classical DHFR inhibitors showing activity against melanoma cells.
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Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
- Naturalius SAS, Bogotá 110221, Colombia
| | - Luis Alberto Gómez
- Laboratorio de Fisiología Molecular, Instituto Nacional de Salud, Bogotá 111321, Colombia
- Department of Physiological Sciences, School of Medicine, Universidad Nacional de Colombia, Bogotá 11001, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Diego M. Riaño-Pachón
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba 05508-060, SP, Brazil
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Identification of Putative Plant-Based ALR-2 Inhibitors to Treat Diabetic Peripheral Neuropathy. Curr Issues Mol Biol 2022; 44:2825-2841. [PMID: 35877418 PMCID: PMC9319673 DOI: 10.3390/cimb44070194] [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: 05/18/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 11/17/2022] Open
Abstract
Diabetic peripheral neuropathy (DPN) is a common diabetes complication (DM). Aldose reductase -2 (ALR-2) is an oxidoreductase enzyme that is most extensively studied therapeutic target for diabetes-related complications that can be inhibited by epalrestat, which has severe adverse effects; hence the discovery of potent natural inhibitors is desired. In response, a pharmacophore model based on the properties of eplarestat was generated. The specified pharmacophore model searched the NuBBEDB database of natural compounds for prospective lead candidates. To assess the drug-likeness and ADMET profile of the compounds, a series of in silico filtering procedures were applied. The compounds were then put through molecular docking and interaction analysis. In comparison to the reference drug, four compounds showed increased binding affinity and demonstrated critical residue interactions with greater stability and specificity. As a result, we have identified four potent inhibitors: ZINC000002895847, ZINC000002566593, ZINC000012447255, and ZINC000065074786, that could be used as pharmacological niches to develop novel ALR-2 inhibitors.
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Castleman P, Szwabowski G, Bowman D, Cole J, Parrill AL, Baker DL. Ligand-based G Protein Coupled Receptor pharmacophore modeling: Assessing the role of ligand function in model development. J Mol Graph Model 2021; 111:108107. [PMID: 34915346 DOI: 10.1016/j.jmgm.2021.108107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022]
Abstract
Integral membrane proteins in the G Protein-Coupled Receptor (GPCR) class are attractive drug development targets. However, computational methods applicable to ligand discovery for many GPCR targets are restricted by limited numbers of known ligands. Pharmacophore models can be developed using variously sized training sets and applied in database mining to prioritize candidate ligands for subsequent validation. This in silico study assessed the impact of key pharmacophore modeling decisions that arise when known ligand numbers for a target of interest are low. GPCR included in this study are the adrenergic alpha-1A, 1D and 2A, adrenergic beta 2 and 3, kappa, delta and mu opioid, serotonin 1A and 2A, and the muscarinic 1 and 2 receptors, all of which have rich ligand data sets suitable to assess the performance of protocols intended for application to GPCR with limited ligand data availability. Impact of ligand function, potency and structural diversity in training set selection was assessed to define when pharmacophore modeling targeting GPCR with limited known ligands becomes viable. Pharmacophore elements and pharmacophore model selection criteria were also assessed. Pharmacophore model assessment was based on percent pharmacophore model generation failure, as well as Güner-Henry enrichment and goodness-of-hit scores. Three of seven pharmacophore element schemes evaluated in MOE 2018.0101, Unified, PCHD, and CHD, showed substantially lower failure rates and higher enrichment scores than the others. Enrichment and GH scores were used to compare construction protocol for pharmacophore models of varying purposes- such as function specific versus nonspecific ligand identification. Notably, pharmacophore models constructed from ligands of mixed functions (agonists and antagonists) were capable of enriching hitlists with active compounds, and therefore can be used when available sets of known ligands are limited in number.
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Affiliation(s)
- P Castleman
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA
| | - G Szwabowski
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA
| | - D Bowman
- The University of Memphis, Department of Mathematics, USA
| | - J Cole
- The University of Memphis, Department of Biological Sciences, USA
| | - A L Parrill
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA
| | - D L Baker
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA.
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11
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Identification of dual inhibitor of phosphodiesterase 1B/10A using structure-based drug design approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Mahajan M, Suryavanshi S, Bhowmick S, Alasmary FA, Almutairi TM, Islam MA, Kaul-Ghanekar R. Matairesinol, an active constituent of HC9 polyherbal formulation, exhibits HDAC8 inhibitory and anticancer activity. Biophys Chem 2021; 273:106588. [PMID: 33848944 DOI: 10.1016/j.bpc.2021.106588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
Histone deacetylase 8 (HDAC8) has emerged as a promising drug target for cancer therapeutics development. HDAC8 has been reported to regulate cancer cell proliferation, invasion and promote metastasis through modulation of cell cycle associated proteins. Of late, phytocompounds have been demonstrated to exhibit anticancer and anti-HDAC8 activity. Here, we have shown the HDAC8 inhibitory potential of an active phytocompound from HC9 (herbal composition-9), a polyherbal anticancer formulation based on the traditional Ayurvedic drug, Stanya Shodhan Kashaya. HC9 was recently reported to exhibit anticancer activity against breast cancer cells through induction of cell cycle arrest, decrease in migration and invasion as well as regulation of inflammation and chromatin modulators. In silico studies such as molecular docking, molecular dynamics (MD) simulation and binding free energy analyses showed greater binding energy values and interaction stability of MA with HDAC8 compared to other phytocompounds of HC9. Interestingly, in vitro validation confirmed the anti-HDAC8 activity of MA. Further, in vitro studies showed that MA significantly decreased the viability of breast and prostate cancer cell lines, thereby confirming its anticancer potential.
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Affiliation(s)
- Minal Mahajan
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India
| | - Snehal Suryavanshi
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India
| | - Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 91 APC Road, Kolkata 700 009, India
| | - Fatmah Ali Alasmary
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Tahani Mazyad Almutairi
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Ruchika Kaul-Ghanekar
- Cancer Research Lab., Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune 411043, Maharashtra, India.
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13
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Zhao L, Che J, Zhang Q, Li Y, Guo X, Chen L, Li H, Cao R, Li X. Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach. Molecules 2020; 25:molecules25225291. [PMID: 33202790 PMCID: PMC7697191 DOI: 10.3390/molecules25225291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022] Open
Abstract
To discover novel inhibitors that target the influenza polymerase basic protein 2 (PB2) cap-binding domain (CBD), commercial ChemBridge compound libraries containing 384,796 compounds were screened using a cascade docking of LibDock-LigandFit-GOLD, and 60 compounds were selected for testing with cytopathic effect (CPE) inhibition assays and surface plasmon resonance (SPR) assay. Ten compounds were identified to rescue cells from H1N1 virus-mediated death at non-cytotoxic concentrations with EC50 values ranging from 0.30 to 67.65 μM and could bind to the PB2 CBD of H1N1 with Kd values ranging from 0.21 to 6.77 μM. Among these, four compounds (11D4, 12C5, 21A5, and 21B1) showed inhibition of a broad spectrum of influenza virus strains, including oseltamivir-resistant ones, the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant strain), the PR/8-I38T mutant (H1N1, recombinant baloxavir-resistant strain), and the influenza B/Lee/40 virus strain. These compounds have novel chemical scaffolds and relatively small molecular weights and are suitable for optimization as lead compounds. Based on sequence and structure comparisons of PB2 CBDs of various influenza virus subtypes, we propose that the Phe323/Gln325, Asn429/Ser431, and Arg355/Gly357 mutations, particularly the Arg355/Gly357 mutation, have a marked impact on the selectivities of PB2 CBD-targeted inhibitors of influenza A and influenza B.
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Affiliation(s)
- Lei Zhao
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China; (L.Z.); (J.C.); (X.G.)
| | - Jinjing Che
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China; (L.Z.); (J.C.); (X.G.)
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China;
| | - Yiming Li
- West China School of Medical, Sichuan University, Chengdu 610041, China;
| | - Xiaojia Guo
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China; (L.Z.); (J.C.); (X.G.)
| | - Lixia Chen
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
- Correspondence: (L.C.); (H.L.); (R.C.); (X.L.); Tel.: +86-024-23986515 (L.C.); +86-27-83692762 (H.L.); +86-10-66930673-717(R.C.); +86-10-66930634 (X.L.)
| | - Hua Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence: (L.C.); (H.L.); (R.C.); (X.L.); Tel.: +86-024-23986515 (L.C.); +86-27-83692762 (H.L.); +86-10-66930673-717(R.C.); +86-10-66930634 (X.L.)
| | - Ruiyuan Cao
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China; (L.Z.); (J.C.); (X.G.)
- Correspondence: (L.C.); (H.L.); (R.C.); (X.L.); Tel.: +86-024-23986515 (L.C.); +86-27-83692762 (H.L.); +86-10-66930673-717(R.C.); +86-10-66930634 (X.L.)
| | - Xingzhou Li
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Road, Beijing 100850, China; (L.Z.); (J.C.); (X.G.)
- Correspondence: (L.C.); (H.L.); (R.C.); (X.L.); Tel.: +86-024-23986515 (L.C.); +86-27-83692762 (H.L.); +86-10-66930673-717(R.C.); +86-10-66930634 (X.L.)
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Vásquez AF, Reyes Muñoz A, Duitama J, González Barrios A. Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. J Biomol Struct Dyn 2020; 39:3285-3299. [DOI: 10.1080/07391102.2020.1763839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes Muñoz
- Grupo de Biología Computacional Ecología Microbiana (BCEM), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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Ligand-based pharmacophore filtering, atom based 3D-QSAR, virtual screening and ADME studies for the discovery of potential ck2 inhibitors. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Discovery of a nanomolar glyoxalase-I inhibitor using integrated ligand-based pharmacophore modeling and molecular docking. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02486-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Debnath S, Debnath T, Bhaumik S, Majumdar S, Kalle AM, Aparna V. Discovery of novel potential selective HDAC8 inhibitors by combine ligand-based, structure-based virtual screening and in-vitro biological evaluation. Sci Rep 2019; 9:17174. [PMID: 31748509 PMCID: PMC6868012 DOI: 10.1038/s41598-019-53376-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor found in children and survival rate is extremely meager. HDAC8, a class I zinc-dependent enzyme, is a potential drug target for treatment of neuroblastoma and T cell lymphoma. Most of the HDAC8 inhibitors discovered till date contains a hydroxamic acid group which acts as a zinc binding group. The high binding affinity to the zinc and other ions results in adverse effects. Also, the non-selective inhibition of HDACs cause a variety of side effects. The objective of this is to identify structurally diverse, non-hydroxamate, novel, potential and selective HDAC8 inhibitors. A number of five featured pharmacophore hypotheses were generated using 32 known selective HDAC8 inhibitors. The hypotheses ADDRR.4 were selected for building 3D QSAR model. This model has an excellent correlation coefficient and good predictive ability, which was employed for virtual screening of Phase database containing 4.3 × 106 molecules. The resultant hits with fitness score >1.0 were optimized using in-silico ADMET (absorption, distribution, metabolism, excretion, and toxicity) and XP glide docking studies. On the basis of pharmacophore matching, interacting amino acid residues, XP glide score, more affinity towards HDAC8 and less affinity towards other HDACs, and ADME results five hits- SD-01, SD-02, SD-03, SD-04 and SD-05 with new structural scaffolds, non-hydroxamate were selected for in vitro activity study. SD-01 and SD-02 were found to be active in the nanomolar (nM) range. SD-01 had considerably good selectivity for HDAC8 over HDAC6 and SD-02 had marginal selectivity for HDAC6 over HDAC8. The compounds SD-01 and SD-02 were found to inhibit HDAC8 at concentrations (IC50) 9.0 nM and 2.7 nM, respectively.
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Affiliation(s)
- Sudhan Debnath
- Department of Chemistry, MBB College, Agartala, Tripura, 799004, India.
| | - Tanusree Debnath
- Department of Chemistry, MBB College, Agartala, Tripura, 799004, India
| | - Samhita Bhaumik
- Department of Chemistry, Women's College, Agartala, Tripura, 799001, India
| | - Swapan Majumdar
- Department of Chemistry, Tripura University, Suryamaninagar, Agartala, Tripura, 799022, India
| | - Arunasree M Kalle
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, TS, 500046, India
| | - Vema Aparna
- Sree Chaitanya Institute of Pharmaceutical Sciences, Karimnagar, 505 527, Andhra Pradesh, India
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18
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Taktak NEM, Badawy MEI. Potential of hydrocarbon and oxygenated monoterpenes against Culex pipiens larvae: Toxicity, biochemical, pharmacophore modeling and molecular docking studies. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 158:156-165. [PMID: 31378352 DOI: 10.1016/j.pestbp.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/25/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Culex pipiens is a main vector for Bancroftian filariasis, Rift Valley Fever and diseases caused by other viruses, leaving several peoples with disabilities. In recent years, plant derived compounds have received much attention as potential alternatives to synthetic chemicals due to their low toxicity to mammals and environmental persistence. Twenty-one monoterpenes from different chemical groups (hydrocarbons and oxygenated products) were evaluated against Culex pipiens larvae. In addition, in vivo biochemical studies including effects on acetylcholine esterase (AChE), acid and alkaline phosphatases (ACP and ALP), total adenosine triphosphatase (ATPase) and gamma-aminobutyric acid transaminase (GABA-T) were investigated. Furthermore, in silico studies including pharmacophore elucidation, ADMET analysis and molecular docking of these compounds were performed. Among all tested monoterpenes, hydrocarbons [p-cymene, (R)-(+)-limonene and (+)-α-pinene], acetates (cinnamyl acetate, citronellyl acetate, eugenyl acetate and terpinyl acetate), alcohols [(±)-β-citronellol and terpineol], aldehydes [citral and (1R)-(-)-myrtenal] and ketone [(R)-(+)-pulegone] exhibited the highest larval toxicity with LC50 = 14.88, 27.97, 26.13, 2.62, 3.81, 2.74, 21.65, 1.64, 21.70, 21.76, 1.68 and 1.90 mg/L after 48 h of exposure, respectively. The compounds proved a significant inhibition of all tested enzymes except total ATPase. The biochemical and molecular docking studies proved that AChE and GABA-T were the main targets for the tested monoterpenes.
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Affiliation(s)
- Nehad E M Taktak
- Department of Tropical Health, High Institute of Public Health, Alexandria University, Alexandria, Egypt.
| | - Mohamed E I Badawy
- Department of Pesticide Chemistry and Technology, Faculty of Agriculture, 21545-El-Shatby, Alexandria University, Alexandria, Egypt
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19
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Uba AI, Weako J, Keskin Ö, Gürsoy A, Yelekçi K. Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:1751-1760. [PMID: 31057077 DOI: 10.1080/07391102.2019.1615989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Histone deacetylase (HDAC) 8 has been implicated as a potential therapeutic target in a variety of cancers, neurodegenerative disorders, metabolic dysregulation and autoimmune and inflammatory diseases. Several nonselective HDAC inhibitors have been co-crystallized with HDAC8. Molecular dynamics (MD) studies may yield valuable information on the structural stabilities of the complexes over time as determined by various pharmacophore features of the co-crystallized inhibitors. Here, using 11 unmodified X-ray crystal structures of human HDAC8 (complexes) structure-based pharmacophore models were built and clustered based on distance - a function of the number of common pharmacophore features and the root-mean-squared displacement between the matching features. Based on this information, a total of seven complexes (1T64, 1W22, 3RQD, 3SFF, 3F0R, 5VI6 and 5FCW) were submitted to unrestrained 50 ns-MD simulations using nanoscale MD (NAMD) software. 1T64 (HDAC8 in complex with TSA) was found to show the highest stability over time, presumably because of the TSA's ability to span HDAC8 catalytic channel and form a strong ionic interaction with zinc metal ion. Other stable complexes were 1W22, 3SFF, 3F0R and 5FCW. However, 3RQD and 5VI6 showed relative instability over 50 ns time period. This may be attributed to bulkiness of the capping groups of both largazole thiol and trapoxin A, making them unable to fit well into the active site of HDAC8. They rather formed steric clashes with residues on loop regions near the entrance to the channel. Thus, 1T64 and similar crystal structures may be good candidates for HDAC8 structural dynamics studies and inhibitor design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
| | - Jackson Weako
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Özlem Keskin
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Attila Gürsoy
- Computational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey
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20
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Liu J, Zhu Y, He Y, Zhu H, Gao Y, Li Z, Zhu J, Sun X, Fang F, Wen H, Li W. Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing. J Biomol Struct Dyn 2019; 38:533-547. [PMID: 30938574 DOI: 10.1080/07391102.2019.1590241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone deacetylases (HDACs), a critical family of epigenetic enzymes, has emerged as a promising target for antitumor drugs. Here, we describe our protocol of virtual screening in identification of novel potential HDAC inhibitors through pharmacophore modeling, 3D-QSAR, molecular docking and molecular dynamics (MD) simulation. Considering the limitation of current virtual screening works, drug repurposing strategy was applied to discover druggable HDAC inhibitor. The ligand-based pharmacophore and 3D-QSAR models were established, and their reliability was validated by different methods. Then, the DrugBank database was screened, followed by molecular docking. MD simulation (100 ns) was performed to further study the stability of ligand binding modes. Finally, results indicated the hit DB03889 with high in silico inhibitory potency was suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yehua Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yufang He
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haohao Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junru Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinjie Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fang Fang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Wen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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21
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Tang JY, Ho Y, Chang CY, Liu HL. Discovery of Novel Irreversible HER2 Inhibitors for Breast Cancer Treatment. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/jbise.2019.124016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Histone deacetylase 8 (HDAC8) and its inhibitors with selectivity to other isoforms: An overview. Eur J Med Chem 2018; 164:214-240. [PMID: 30594678 DOI: 10.1016/j.ejmech.2018.12.039] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/04/2018] [Accepted: 12/16/2018] [Indexed: 01/08/2023]
Abstract
The histone deacetylases (HDACs) enzymes provided crucial role in transcriptional regulation of cells through deacetylation of nuclear histone proteins. Discoveries related to the HDAC8 enzyme activity signified the importance of HDAC8 isoform in cell proliferation, tumorigenesis, cancer, neuronal disorders, parasitic/viral infections and other epigenetic regulations. The pan-HDAC inhibitors can confront these conditions but have chances to affect epigenetic functions of other HDAC isoforms. Designing of selective HDAC8 inhibitors is a key feature to combat the pathophysiological and diseased conditions involving the HDAC8 activity. This review is concerned about the structural and positional aspects of HDAC8 in the HDAC family. It also covers the contributions of HDAC8 in the pathophysiological conditions, a preliminary discussion about the recent scenario of HDAC8 inhibitors. This review might help to deliver the structural, functional and computational information in order to identify and design potent and selective HDAC8 inhibitors for target specific treatment of diseases involving HDAC8 enzymatic activity.
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23
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Uba AI, Yelekçi K. Pharmacophore-based virtual screening for identification of potential selective inhibitors of human histone deacetylase 6. Comput Biol Chem 2018; 77:318-330. [PMID: 30463049 DOI: 10.1016/j.compbiolchem.2018.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
Histone deacetylase (HDAC) 6 plays a role in oncogenic transformation and cancer metastasis via tubulin deacetylation, making it a critical target for anticancer drug design. However, lack of selectivity shown by many of the current HDAC6 inhibitors in clinical use and trials prompts the continuous search for selective inhibitors. Here, 10 pharmacophore hypotheses were developed based on the 3D common features of training set of 20 HDAC inhibitors in clinical use and trials. The hypotheses were validated using a test set of another 20 HDAC inhibitors along with 400 inactive (decoys) molecules based on Güner-Henry pharmacophore scoring method. Hypothesis 1 consisting of 1 H-bond donor, 1 H-bond acceptor and 2 hydrophobic features, was used to screen "DruglikeDiverse" database using Biovia Discovery Studio 4.5. The top 10 hit compounds were selected based on the pharmacophore fit values (>3.00). Their binding affinity against HDAC6 compared to class I HDACs (1, 2, 3 & 8) and a class IIa member (HDAC7), was calculated by molecular docking using AutoDock4. The stability of binding modes of 2 potential HDAC6-selective inhibitors (ENA501965 and IBS399024) was examined by 30 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software. Both ligands showed potential stability in HDAC6 active site over time. Therefore, these may provide additional scaffolds for further optimization towards the design of safe, potent and selective HDAC6 inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey; Centre for Biotechnology Research, Bayero University, P.M.B 3011, B.U.K road, Kano, Nigeria
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey.
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24
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Sangwan R, Rajan R, Mandal PK. HDAC as onco target: Reviewing the synthetic approaches with SAR study of their inhibitors. Eur J Med Chem 2018; 158:620-706. [DOI: 10.1016/j.ejmech.2018.08.073] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/09/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023]
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25
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Kim S, Lee Y, Kim S, Lee SJ, Heo PK, Kim S, Kwon YJ, Lee KW. Identification of Novel Human HDAC8 Inhibitors by Pharmacophore-based Virtual Screening and Density Functional Theory Approaches. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seokmin Kim
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Yuno Lee
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Songmi Kim
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Sang Jik Lee
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Phil Kyeong Heo
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Siu Kim
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
| | - Yong Jung Kwon
- Department of Chemical Engineering; Kangwon National University; Chunchon 200-701 Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS); Gyeongsang National University (GNU); Jinju 52828 Republic of Korea
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26
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Uba Aİ, Yelekçi K. Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors. Turk J Biol 2017; 41:901-918. [PMID: 30814855 DOI: 10.3906/biy-1701-26] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. "Classical" HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivity.
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Affiliation(s)
- Abdullahi İbrahim Uba
- Center for Biotechnology Research, Bayero University Kano , Nigeria.,Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University , İstanbul , Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University , İstanbul , Turkey
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Target identification, lead optimization and antitumor evaluation of some new 1,2,4-triazines as c-Met kinase inhibitors. Bioorg Chem 2017; 73:154-169. [DOI: 10.1016/j.bioorg.2017.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 11/19/2022]
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Prachayasittikul V, Prathipati P, Pratiwi R, Phanus-Umporn C, Malik AA, Schaduangrat N, Seenprachawong K, Wongchitrat P, Supokawej A, Prachayasittikul V, Wikberg JES, Nantasenamat C. Exploring the epigenetic drug discovery landscape. Expert Opin Drug Discov 2017; 12:345-362. [PMID: 28276705 DOI: 10.1080/17460441.2017.1295954] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Epigenetic modification has been implicated in a wide range of diseases and the ability to modulate such systems is a lucrative therapeutic strategy in drug discovery. Areas covered: This article focuses on the concepts and drug discovery aspects of epigenomics. This is achieved by providing a survey of the following concepts: (i) factors influencing epigenetics, (ii) diseases arising from epigenetics, (iii) epigenetic enzymes as druggable targets along with coverage of existing FDA-approved drugs and pharmacological agents, and (iv) drug repurposing/repositioning as a means for rapid discovery of pharmacological agents targeting epigenetics. Expert opinion: Despite significant interests in targeting epigenetic modifiers as a therapeutic route, certain classes of target proteins are heavily studied while some are less characterized. Thus, such orphan target proteins are not yet druggable with limited report of active modulators. Current research points towards a great future with novel drugs directed to the many complex multifactorial diseases of humans, which are still often poorly understood and difficult to treat.
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Affiliation(s)
- Veda Prachayasittikul
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Philip Prathipati
- b National Institutes of Biomedical Innovation, Health and Nutrition , Osaka , Japan
| | - Reny Pratiwi
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Chuleeporn Phanus-Umporn
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aijaz Ahmad Malik
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Nalini Schaduangrat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Kanokwan Seenprachawong
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Prapimpun Wongchitrat
- d Center for Research and Innovation, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aungkura Supokawej
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Virapong Prachayasittikul
- e Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Jarl E S Wikberg
- f Department of Pharmaceutical Biosciences , Uppsala University , Uppsala , Sweden
| | - Chanin Nantasenamat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
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Sinha S, Goyal S, Somvanshi P, Grover A. Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach. Front Neurosci 2017; 10:606. [PMID: 28119557 PMCID: PMC5223442 DOI: 10.3389/fnins.2016.00606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
Spinocerebellar ataxia (SCA-2) type-2 is a rare neurological disorder among the nine polyglutamine disorders, mainly caused by polyQ (CAG) trinucleotide repeats expansion within gene coding ataxin-2 protein. The expanded trinucleotide repeats within the ataxin-2 protein sequesters transcriptional cofactors i.e., CREB-binding protein (CBP), Ataxin-2 binding protein 1 (A2BP1) leading to a state of hypo-acetylation and transcriptional repression. Histone de-acetylases inhibitors (HDACi) have been reported to restore transcriptional balance through inhibition of class IIa HDAC's, that leads to an increased acetylation and transcription as demonstrated through in-vivo studies on mouse models of Huntington's. In this study, 61 di-aryl cyclo-propanehydroxamic acid derivatives were used for developing three dimensional (3D) QSAR and pharmacophore models. These models were then employed for screening and selection of anti-ataxia compounds. The chosen QSAR model was observed to be statistically robust with correlation coefficient (r2) value of 0.6774, cross-validated correlation coefficient (q2) of 0.6157 and co-relation coefficient for external test set (pred_r2) of 0.7570. A high F-test value of 77.7093 signified the robustness of the model. Two potential drug leads ZINC 00608101 (SEI) and ZINC 00329110 (ACI) were selected after a coalesce procedure of pharmacophore based screening using the pharmacophore model ADDRR.20 and structural analysis using molecular docking and dynamics simulations. The pharmacophore and the 3D-QSAR model generated were further validated for their screening and prediction ability using the enrichment factor (EF), goodness of hit (GH), and receiver operating characteristics (ROC) curve analysis. The compounds SEI and ACI exhibited a docking score of −10.097 and −9.182 kcal/mol, respectively. An evaluation of binding conformation of ligand-bound protein complexes was performed with MD simulations for a time period of 30 ns along with free energy binding calculations using the g_mmpbsa technique. Prediction of inhibitory activities of the two lead compounds SEI (7.53) and ACI (6.84) using the 3D-QSAR model reaffirmed their inhibitory characteristics as potential anti-ataxia compounds.
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Affiliation(s)
- Siddharth Sinha
- Department of Biotechnology, TERI University New Delhi, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University Tonk, India
| | | | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University New Delhi, India
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A comparative study based on docking and molecular dynamics simulations over HDAC-tubulin dual inhibitors. J Mol Graph Model 2016; 70:170-180. [DOI: 10.1016/j.jmgm.2016.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 09/22/2016] [Accepted: 10/06/2016] [Indexed: 11/23/2022]
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Chen WL, Wang ZH, Feng TT, Li DD, Wang CH, Xu XL, Zhang XJ, You QD, Guo XK. Discovery, design and synthesis of 6H-anthra[1,9-cd]isoxazol-6-one scaffold as G9a inhibitor through a combination of shape-based virtual screening and structure-based molecular modification. Bioorg Med Chem 2016; 24:6102-6108. [PMID: 27720557 DOI: 10.1016/j.bmc.2016.09.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 01/29/2023]
Abstract
Protein lysine methyltransferase G9a is widely considered as an appealing antineoplastic target. Herein we present an integrated workflow combining shape-based virtual screening and structure-based molecular modification for the identification of novel G9a inhibitors. The shape-based similarity screening through ROCS overlay on the basis of the structure of UNC0638 was performed to identify CPUY074001 contained a 6H-anthra[1,9-cd]isoxazol-6-one scaffold as a hit. Analysis of the binding mode of CPUY074001 with G9a and 3D-QSAR results, two series compounds were designed and synthesized. The derivatives were confirmed to be active by in vitro assay and the SAR was explored by docking stimulations. Besides, several analogues showed acceptable anti-proliferative effects against several cancer cell lines. Among them, CPUY074020 displayed potent dual G9a inhibitory activity and anti-proliferative activity. Furthermore, CPUY074020 induced cell apoptosis in a dose-dependent manner and displayed a significant decrease in dimethylation of H3K9. Simultaneously, CPUY074020 showed reasonable in vivo PK properties. Altogether, our workflow supplied a high efficient strategy in the identification of novel G9a inhibitors. Compounds reported here can serve as promising leads for further study.
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Affiliation(s)
- Wei-Lin Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Zhi-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Tao-Tao Feng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Dong-Dong Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Chu-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Li Xu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Jin Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiao-Ke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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32
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A combined pharmacophore modeling, 3D QSAR, virtual screening, molecular docking, and ADME studies to identify potential HDAC8 inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1652-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Roche J, Bertrand P. Inside HDACs with more selective HDAC inhibitors. Eur J Med Chem 2016; 121:451-483. [PMID: 27318122 DOI: 10.1016/j.ejmech.2016.05.047] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 01/08/2023]
Abstract
Inhibitors of histone deacetylases (HDACs) are nowadays part of the therapeutic arsenal mainly against cancers, with four compounds approved by the Food and Drug Administration. During the last five years, several groups have made continuous efforts to improve this class of compounds, designing more selective compounds or compounds with multiple capacities. After a survey of the HDAC biology and structures, this review summarizes the results of the chemists working in this field, and highlights when possible the behavior of the molecules inside their targets.
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Affiliation(s)
- Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions, Equipe « SEVE Sucres & Echanges Végétaux-Environnement », Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Philippe Bertrand
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B28, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France.
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Santos-Garcia L, Assis LC, Silva DR, Ramalho TC, da Cunha EF. QSAR analysis of nicotinamidic compounds and design of potential Bruton’s tyrosine kinase (Btk) inhibitors. J Biomol Struct Dyn 2016; 34:1421-40. [DOI: 10.1080/07391102.2015.1070750] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Letícia Santos-Garcia
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Letícia C. Assis
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Daniela R. Silva
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
| | - Elaine F.F. da Cunha
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil
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Nagamani S, Muthusamy K, Marshal JJ. E-pharmacophore filtering and molecular dynamics simulation studies in the discovery of potent drug-like molecules for chronic kidney disease. J Biomol Struct Dyn 2016; 34:2233-2250. [PMID: 26513595 DOI: 10.1080/07391102.2015.1111168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic kidney disease (CKD) is a prominent health issue reported globally. The level of the vitamin D receptor (VDR) and cytochrome P450 enzyme 24-hydroxylase (CYP24A1) are crucial in the pathogenesis of secondary hyperparathyroidism (sHPT) in CKD. An elevated expression of the CYP24A1 leads to the deficiency of vitamin D and resistance to vitamin D therapy. Hence, VDR agonists and CYP24A1 antagonists are suggested to CKD patients for the management of biochemical complications. CTA-018 is a recently reported analog and acts as a potent CYP24A1 inhibitor. It inhibits CYP24A1 with an IC50 27 ± 6 nM, about 10 times more potentially than the non-selective inhibitor ketoconazole (253 ± 20 nM), and it is also been reported to induce the VDR expression. Thus, CTA-018 is under clinical trial among CKD patients. In this study, combined molecular docking and pharmacophore filtering were employed to identify compounds better than CTA-018. A huge set of 9127 compounds from Sweet Lead database were docked into the active site of VDR using Glide XP program. E-pharmacophore was developed from both the targets along with CTA-018. The compounds retrieved from the two different pharmacophore-based screening were re-docked into the active site of CYP24A1. The hits that bind well at both the active sites and matched with the pharmacophore models were considered as possible dual functional molecules against VDR and CYP24A1. Further, molecular dynamics simulation and subsequent energy decomposition analyses were also performed to study the role of specific amino acids in the active site of both VDR and CYP24A1.
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Affiliation(s)
- Selvaraman Nagamani
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
| | | | - J John Marshal
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
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36
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Tseng TS, Chuang SM, Hsiao NW, Chen YW, Lee YC, Lin CC, Huang C, Tsai KC. Discovery of a potent cyclooxygenase-2 inhibitor, S4, through docking-based pharmacophore screening, in vivo and in vitro estimations. MOLECULAR BIOSYSTEMS 2016; 12:2541-51. [DOI: 10.1039/c6mb00229c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclooxygenase (COX; EC: 1.14.99.1), the key enzyme in prostaglandin production in the human body, is a major pharmacological target for developing anti-inflammatory agents.
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Affiliation(s)
- Tien-Sheng Tseng
- National Research Institute of Chinese Medicine
- Ministry of Health and Welfare
- Taipei
- Taiwan
- Institute of Biomedical Sciences
| | - Show-Mei Chuang
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
| | - Nai-Wan Hsiao
- Institute of Biotechnology
- National Changhua University of Education
- Changhua
- Taiwan
| | | | - Yu-Ching Lee
- The Center of Translational Medicine
- Taipei Medical University
- Taipei
- Taiwan
- The Ph.D. Program for Medical Biotechnology
| | - Chi-Chen Lin
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
| | - Cheng Huang
- National Research Institute of Chinese Medicine
- Ministry of Health and Welfare
- Taipei
- Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine
- Ministry of Health and Welfare
- Taipei
- Taiwan
- The Ph.D. Program for Medical Biotechnology
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Xiao J, Fang M, Shi Y, Chen H, Shen B, Chen J, Lao X, Xu H, Zheng H. Identification and Validation Novel of VIM-2 Metallo-β-lactamase Tripeptide Inhibitors. Mol Inform 2015; 34:559-67. [DOI: 10.1002/minf.201400178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/16/2015] [Indexed: 11/07/2022]
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38
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Gupta SP. QSAR Studies on Hydroxamic Acids: A Fascinating Family of Chemicals with a Wide Spectrum of Activities. Chem Rev 2015; 115:6427-90. [DOI: 10.1021/cr500483r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satya P. Gupta
- Department of Applied Sciences, National Institute of Technical Teachers’ Training and Research, Shamla
Hills, Bhopal-462002, India
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39
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Hou X, Du J, Liu R, Zhou Y, Li M, Xu W, Fang H. Enhancing the Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Customized ZBG Features: A Case Study Using Histone Deacetylase 8. J Chem Inf Model 2015; 55:861-71. [DOI: 10.1021/ci500762z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Jinan, Shandong 250117, China
| | - Renshuai Liu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yi Zhou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Wenfang Xu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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40
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Hurmach VV, Taras Shevchenko National University of Kyiv, Ukraine. Application of the methods of molecular modeling to the search for new biologically active substances. UKRAINIAN BIOCHEMICAL JOURNAL 2015. [DOI: 10.15407/ubj87.01.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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41
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Niu M, Wang F, Li F, Dong Y, Gu Y. Establishment of a screening protocol for identification of aminopeptidase N inhibitors. J Taiwan Inst Chem Eng 2014; 49:19-26. [PMID: 32336998 PMCID: PMC7172515 DOI: 10.1016/j.jtice.2014.11.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/09/2014] [Accepted: 11/30/2014] [Indexed: 11/25/2022]
Abstract
Two pharmacophore models have been developed. Virtual screening was performed by the pharmacophore models and docking. Six selected hits were discovered to have inhibitory activities.
Inhibitors of aminopeptidase N (APN) have been thought as potential drugs for the treatment of tumor angiogenesis, invasion and metastasis and a considerable number of APN inhibitors have been reported recently. To clarify the essential structure–activity relationship for the APN inhibitors as well as identify new potent leads against APN, pharmacophore models were established using structure- and common feature-based approaches and validated with a database of active and inactive compounds. These validated pharmacophores were then used in database screening for novel virtual leads. The hit compounds were further subjected to molecular docking studies to refine the retrieved hits. Finally, six structurally diverse compounds that showed strong interactions with the key amino acids and the zinc ion were selected for biological evaluation, where two hits showed more than 70% inhibition against APN at 60 μM concentration. The evaluation results show the potential of our screening approach in identifying APN inhibitors.
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Affiliation(s)
- Miaomiao Niu
- Department of Biomedical Engineering, School of Life Science and Technology, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Fengzhen Wang
- Department of Biomedical Engineering, School of Life Science and Technology, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Li
- Department of Biomedical Engineering, School of Life Science and Technology, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yaru Dong
- Department of Biomedical Engineering, School of Life Science and Technology, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yueqing Gu
- Department of Biomedical Engineering, School of Life Science and Technology, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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42
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Hou X, Li R, Li K, Yu X, Sun JP, Fang H. Fast Identification of Novel Lymphoid Tyrosine Phosphatase Inhibitors Using Target–Ligand Interaction-Based Virtual Screening. J Med Chem 2014; 57:9309-22. [PMID: 25372368 DOI: 10.1021/jm500692u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Rong Li
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kangshuai Li
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yu
- Department
of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jin-Peng Sun
- Key
Laboratory Experimental Teratology of the Ministry of Education and
Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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43
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Kalyaanamoorthy S, Chen YPP. A steered molecular dynamics mediated hit discovery for histone deacetylases. Phys Chem Chem Phys 2014; 16:3777-91. [PMID: 24429775 DOI: 10.1039/c3cp53511h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The inhibitors of class I histone deacetylases (HDACIs) have gained significant interest in cancer therapeutics. Virtual high throughput screening (vHTS) is one of the popular approaches used in the identification of novel scaffolds of HDACIs. However, an accurate description of ligand-protein flexibilities in the vHTS remains challenging. In this work, we implement an integrated approach, which combines the vHTS with the 'state-of-the-art' steered molecular dynamics (SMD). This approach serves as an efficient tool to identify potential hits and characterize their binding potencies against the class I HDACs in a flexible solvent environment. A hybrid pharmacophore-based and structure-based vHTS method identifies the hits with more favourable physico-chemical features against the class I HDACs. Our pharmacophore-based screening enhanced the quality of the vHTS outcomes. Further, the molecular interactions between the hits and the HDACs are investigated using the SMD-driven force profiles, which in turn resulted in filtering the hits with higher binding potencies against the HDACs. Our results, therefore, reveal that vHTS and SMD can be a complementary and effective analytical tool for accelerating the hit identification phase in structure-based drug design.
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Affiliation(s)
- Subha Kalyaanamoorthy
- Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia.
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Xu XL, Sun HP, Liu F, Jia JM, Guo XK, Pan Y, Huang HZ, Zhang XJ, You QD. Discovery and Bioevaluation of Novel Pyrazolopyrimidine Analogs as Competitive Hsp90 Inhibitors Through Shape-Based Similarity Screening. Mol Inform 2014; 33:293-306. [PMID: 27485776 DOI: 10.1002/minf.201300150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/13/2014] [Indexed: 12/14/2022]
Abstract
Hsp90 as a promising therapeutic target for the treatment of cancer has received great attention. Many Hsp90 inhibitors such as BIIB021 and CUDC-305 have been in clinical. In this paper shape-based similarity screening through ROCS overlays on the basis of CUDC-305, BIIB021, PU-H71 and PU-3 were performed to discover HSP90 inhibitors. A set of 19 novel pyrazolopyrimidine analogues was identified and evaluated on enzyme level and cell-based level as Hsp90 inhibitors. The compound HDI4-04 with IC50 0.35 µM in the Hsp90 ATP hydrolysis assay exhibited potent cytotoxicity against five human cancer cell lines. Western blot analysis and Hsp70 luciferase reporter assay further confirmed that HDI4-04 targeted the Hsp90 protein folding machinery. And according to the biological assay, the SAR was discussed and summarized, which will guide us for further optimization of these compounds.
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Affiliation(s)
- Xiao-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Peng Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216
| | - Fang Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jian-Min Jia
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Ke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yang Pan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Ze Huang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Jin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi-Dong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351. , .,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China. , .,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216. ,
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Structure-based pharmacophore modeling and virtual screening to identify novel inhibitors for anthrax lethal factor. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0947-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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46
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Wang JL, Liu HL, Zhou ZL, Chen WH, Ho Y. Discovery of novel 5α-reductase type II inhibitors by pharmacophore modelling, virtual screening, molecular docking and molecular dynamics simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.878865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Kalva S, Azhagiya Singam ER, Rajapandian V, Saleena LM, Subramanian V. Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies. J Mol Graph Model 2014; 49:25-37. [PMID: 24473069 DOI: 10.1016/j.jmgm.2013.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 12/17/2013] [Accepted: 12/20/2013] [Indexed: 12/21/2022]
Abstract
Matrix metalloproteinase-9 (MMP-9) is an attractive target for anticancer therapy. In the present study ligand based pharmacophore modeling was performed to elucidate the structural elements for a diverse class of MMP-9 inhibitors. The pharmacophore model was validated through Güner-Henry (GH) scoring method. The final pharmacophore model consisted of three hydrogen bond acceptors (HBA), and two ring aromatic regions (RA). This model was utilized to screen the natural compound database to seek novel compounds as MMP-9 inhibitors. The identified hits were validated using molecular docking and molecular dynamics simulation studies. Finally, one compound named Hinokiflavone from Juniperus communis had high binding free energy of -26.54kJ/mol compared with the known inhibitors of MMP-9. Cytotoxicity for hinokiflavone was evaluated by MTT assay. Inhibition of MMP-9 in the presence of hinokiflavone was detected by gelatin zymography and gelatinolytic inhibition assay. Results revealed that the natural compounds derived based on the developed pharmacophore model would be useful for further design and development of MMP-9 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India
| | - E R Azhagiya Singam
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - Lilly M Saleena
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India.
| | - V Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India.
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48
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Sun H, Xu X, Wu X, Zhang X, Liu F, Jia J, Guo X, Huang J, Jiang Z, Feng T, Chu H, Zhou Y, Zhang S, Liu Z, You Q. Discovery and design of tricyclic scaffolds as protein kinase CK2 (CK2) inhibitors through a combination of shape-based virtual screening and structure-based molecular modification. J Chem Inf Model 2013; 53:2093-102. [PMID: 23937544 DOI: 10.1021/ci400114f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinase CK2 (CK2), a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates, serves as an attractive anticancer target. One of its most potent inhibitors, CX-4945, has entered a phase I clinical trial. Herein we present an integrated workflow combining shape-based virtual screening for the identification of novel CK2 inhibitors. A shape-based model derived from CX-4945 was built, and the subsequent virtual screening led to the identification of several novel scaffolds with high shape similarity to that of CX-4945. Among them two tricyclic scaffolds named [1,2,4]triazolo[4,3-c]quinazolin and [1,2,4]triazolo[4,3-a]quinoxalin attracted us the most. Combining strictly chemical similarity analysis, a second-round shape-based screening was performed based on the two tricyclic scaffolds, leading to 28 derivatives. These compounds not only targeted CK2 with potent and dose-dependent activities but also showed acceptable antiproliferative effects against a series of cancer cell lines. Our workflow supplies a high efficient strategy in the identification of novel CK2 inhibitors. Compounds reported here can serve as ideal leads for further modifications.
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Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Kalva S, Saranyah K, Suganya PR, Nisha M, Saleena LM. Potent inhibitors precise to S1' loop of MMP-13, a crucial target for osteoarthritis. J Mol Graph Model 2013; 44:297-310. [PMID: 23938376 DOI: 10.1016/j.jmgm.2013.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/21/2013] [Accepted: 06/23/2013] [Indexed: 11/30/2022]
Abstract
Matrix metalloproteinase-13 (MMP-13) is the primary MMP involved in cartilage degradation through its particular ability to cleave type-II collagen. This protein is expressed by chondrocytes and synovial cells in human osteoarthritis and rheumatoid arthritis; hence, it is an attractive target for the treatment of arthritic diseases. Currently available inhibitors lack specificity for metalloproteinase because of a common Zn binding site in MMPs; thus, there is a need to identify selective MMP-13 inhibitors for osteoarthritis therapy. Because selectivity is the major concern, both ligand-based and protein-based pharmacophore methodologies were used to identity potent and selective MMP-13 inhibitors. Different hypotheses were validated, and the best hypothesis was used to screen Zinc (natural and chemical) databases to seek novel scaffolds as MMP-13 inhibitors. The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC). In addition, potent inhibitors were selected based on two criteria: a similar binding mode as that of the active site PB3 crystal ligand and crucial amino acid interactions that are catalytically important for the function of MMP-13. The candidate potent inhibitors ZINC 02535232, ZINC 08399795, ZINC 12419118 and ZINC 00624580 nearly reproduced the H-bond interactions formed in the crystal structure of 1XUC with reasonable RMSD values exhibiting a novel interaction pattern that was not previously observed in MMP-13 inhibitors. The identified potent hits with diverse chemical scaffolds may be useful in designing new MMP-13 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur, Kancheepuram District, Chennai 603203, India
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Kumar RB, Suresh MX. Pharmacophore mapping based inhibitor selection and molecular interaction studies for identification of potential drugs on calcium activated potassium channel blockers, tamulotoxin. Pharmacogn Mag 2013; 9:89-95. [PMID: 23772102 PMCID: PMC3680861 DOI: 10.4103/0973-1296.111239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 04/06/2013] [Accepted: 04/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background: Tamulotoxin (TmTx) from Buthus tamulus was found to be a highly venomous toxin which accelerates the neurotransmitter release that directly affects the cardiovascular tissues and the respiratory system leading to death. TmTx from red Indian scorpion is a crucial inhibitor for Ca2+ activated K+ channel in humans. Objective: The study is aimed at the identification of potential inhibitors of TmTx through pharmacophore based inhibitor screening and understanding the molecular level interactions. Materials and Method: The potential inhibitors for TmTx were identified using pharmacophore model based descriptor information present in existing drugs with the analysis of pharmacokinetic properties. The compounds with good ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) descriptors were subjected to molecular interaction studies. The stability of bound toxin-inhibitor complex was studied using molecular dynamics simulation over a period of one nanosecond. Results: From a dataset of 3406 compounds, few compounds were selected as potential inhibitors based on the generated best pharmacophore models, pharmacokinetic analysis, molecular docking and molecular dynamics studies. Conclusion: In conclusion, two compounds containing better inhibition properties against TmTx are suggested to be better lead molecules for drug development in future and this study will help us to explore more inhibitors from natural origin against tamulotoxin.
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Affiliation(s)
- R Barani Kumar
- Department of Bioinformatics, Sathyabama University, Chennai, India
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