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Kim JH, Jeong JH. Structure-Activity Relationship Studies Based on 3D-QSAR CoMFA/CoMSIA for Thieno-Pyrimidine Derivatives as Triple Negative Breast Cancer Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227974. [PMID: 36432075 PMCID: PMC9698756 DOI: 10.3390/molecules27227974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/04/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022]
Abstract
Triple-negative breast cancer (TNBC) is defined as a kind of breast cancer that lacks estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER2). This cancer accounts for 10-15% of all breast cancers and has the features of high invasiveness and metastatic potential. The treatment regimens are still lacking and need to develop novel inhibitors for therapeutic strategies. Three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses, based on a series of forty-seven thieno-pyrimidine derivatives, were performed to identify the key structural features for the inhibitory biological activities. The established comparative molecular field analysis (CoMFA) presented a leave-one-out cross-validated correlation coefficient q2 of 0.818 and a determination coefficient r2 of 0.917. In comparative molecular similarity indices analysis (CoMSIA), a q2 of 0.801 and an r2 of 0.897 were exhibited. The predictive capability of these models was confirmed by using external validation and was further validated by the progressive scrambling stability test. From these results of validation, the models were determined to be statistically reliable and robust. This study could provide valuable information for further optimization and design of novel inhibitors against metastatic breast cancer.
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Rac1 as a Target to Treat Dysfunctions and Cancer of the Bladder. Biomedicines 2022; 10:biomedicines10061357. [PMID: 35740379 PMCID: PMC9219850 DOI: 10.3390/biomedicines10061357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Bladder pathologies, very common in the aged population, have a considerable negative impact on quality of life. Novel targets are needed to design drugs and combinations to treat diseases such as overactive bladder and bladder cancers. A promising new target is the ubiquitous Rho GTPase Rac1, frequently dysregulated and overexpressed in bladder pathologies. We have analyzed the roles of Rac1 in different bladder pathologies, including bacterial infections, diabetes-induced bladder dysfunctions and bladder cancers. The contribution of the Rac1 protein to tumorigenesis, tumor progression, epithelial-mesenchymal transition of bladder cancer cells and their metastasis has been analyzed. Small molecules selectively targeting Rac1 have been discovered or designed, and two of them—NSC23766 and EHT 1864—have revealed activities against bladder cancer. Their mode of interaction with Rac1, at the GTP binding site or the guanine nucleotide exchange factors (GEF) interaction site, is discussed. Our analysis underlines the possibility of targeting Rac1 with small molecules with the objective to combat bladder dysfunctions and to reduce lower urinary tract symptoms. Finally, the interest of a Rac1 inhibitor to treat advanced chemoresistance prostate cancer, while reducing the risk of associated bladder dysfunction, is discussed. There is hope for a better management of bladder pathologies via Rac1-targeted approaches.
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Frankel J, Staskin D, Varano S, Kennelly MJ, Jankowich RA, Haag-Molkenteller C. An Evaluation of the Efficacy and Safety of Vibegron in the Treatment of Overactive Bladder. Ther Clin Risk Manag 2022; 18:171-182. [PMID: 35264853 PMCID: PMC8901416 DOI: 10.2147/tcrm.s310371] [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: 09/11/2021] [Accepted: 02/13/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacologic treatment for overactive bladder (OAB), which is characterized by bothersome symptoms such as urgency and urge urinary incontinence (UUI), includes anticholinergics and β3-adrenergic receptor agonists. Anticholinergics are associated with adverse effects including dry mouth, constipation, cognitive impairment, and increased risk of dementia. Therefore, the drug class of β3-adrenergic receptor agonists may represent an effective, safe treatment option. Vibegron, a β3-adrenergic receptor agonist, was approved for use in Japan (2018) and the United States (2020). Over the past 3 years, 2 phase 3 trials (EMPOWUR, EMPOWUR extension) have been conducted with once-daily vibegron 75 mg for the treatment of OAB, and additional secondary and subgroup analyses have detailed the efficacy and safety of vibegron. In the international phase 3 EMPOWUR trial, treatment with vibegron was associated with significant improvements compared with placebo in efficacy outcomes of micturition frequency, UUI episodes, urgency episodes, and volume voided as early as week 2 that were sustained throughout the 12-week trial. The 40-week EMPOWUR extension study, following the 12-week treatment period, demonstrated sustained efficacy in patients receiving vibegron for 52 weeks. Treatment with vibegron was also associated with improvements in patient-reported measures of quality of life. Across studies, vibegron was generally safe and well tolerated. A separate, dedicated ambulatory blood pressure monitoring study showed that treatment with vibegron was not associated with clinically meaningful effects on blood pressure or heart rate. Across all studies, vibegron was efficacious, safe, and well tolerated and thus represents a valuable treatment option for patients with OAB. Here, nearly 1 year after US approval, we review the published data on efficacy and safety of vibegron 75 mg for the treatment of OAB.
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Affiliation(s)
| | - David Staskin
- Tufts University School of Medicine, Boston, MA, USA
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Chen XZ, Huang Q, Yu XY, Dai C, Shen Y, Lin ZH. Insights into the structural requirements of PKCζ inhibitors as potential anti-arthritis agents based on 3D-QSAR, homology modeling and docking approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Yamada S, Chimoto J, Shiho M, Okura T, Morikawa K, Kagota S, Shinozuka K. Muscarinic receptor binding activity in rat tissues by vibegron and prediction of its receptor occupancy levels in the human bladder. Int J Urol 2021; 28:1298-1303. [PMID: 34545632 DOI: 10.1111/iju.14696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To examine the effects of vibegron, a selective β3 -adrenoceptor agonist, used to treat overactive bladder, on muscarinic receptors in the rat bladder, and to predict the occupancy levels of muscarinic receptors by vibegron in the bladders of humans orally administered a clinical dose. METHODS Muscarinic receptors in the rat bladder and other tissues were examined by a radioligand binding assay using [N-methyl-3 H]scopolamine chloride. The occupancy levels of muscarinic receptors by vibegron in bladders of humans after its oral administration were predicted from the estimation of unbound concentrations in human plasma and urine in the literature. RESULTS Vibegron (0.1-100 μmol/L) inhibited specific [N-methyl-3 H]scopolamine chloride binding in the bladder and other tissues of rats in a concentration-dependent manner. The 50% inhibitory concentration value of vibegron in the bladder was approximately twofold higher than that in the heart, and approximately 315- and 3.5-fold lower than those in the submaxillary gland and brain, respectively. Therefore, the binding affinity of vibegron for muscarinic receptors was higher in the heart and bladder than in the submaxillary gland and brain. By using the rat bladder receptor binding affinity, occupancy levels of muscarinic receptors in the human bladder were predicted to be 51-91% until 24 h after its oral administration at 50 mg of vibegron. CONCLUSIONS This is the first study to suggest that vibegron binds to muscarinic receptors in the rat bladder and other tissues, with a potentially higher affinity for the M2 subtype than the M1 and M3 subtypes. These results might be clinically relevant for pharmacotherapy with vibegron for overactive bladder.
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Affiliation(s)
- Shizuo Yamada
- Center for Pharma-Food Research, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Junko Chimoto
- Center for Pharma-Food Research, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Mizuki Shiho
- Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Takashi Okura
- Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kana Morikawa
- Department of Pharmacology II, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Satomi Kagota
- Department of Pharmacology II, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Kazumasa Shinozuka
- Department of Pharmacology II, School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Japan
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6
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Luo D, Tong JB, Zhang X, Xiao XC, Bian S. Computational strategies towards developing novel SARS-CoV-2 M pro inhibitors against COVID-19. J Mol Struct 2021; 1247:131378. [PMID: 34483363 PMCID: PMC8398673 DOI: 10.1016/j.molstruc.2021.131378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains to be a serious threat due to the lack of a specific therapeutic agent. Computational methods are particularly suitable for rapidly fight against SARS-CoV-2. This present research aims to systematically explore the interaction mechanism of a series of novel bicycloproline-containing SARS-CoV-2 Mpro inhibitors through integrated computational approaches. We designed six structurally modified novel SARS-CoV-2 Mpro inhibitors based on the QSAR study. The four designed compounds with higher docking scores were further explored through molecular docking, molecular dynamics (MD) simulations, free energy calculations, and residual energy contributions estimated by the MM-PBSA approach, with comparison to compound 23(PDB entry 7D3I). This research not only provides robust QSAR models as valuable screening tools for the development of anti-COVID-19 drugs, but also proposes the newly designed SARS-CoV-2 Mpro inhibitors with nanomolar activities that can be potentially used for further characterization to treat SARS-CoV-2 virus.
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Affiliation(s)
- Ding Luo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China
| | - Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China
| | - Xing Zhang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China
| | - Xue-Chun Xiao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China
| | - Shuai Bian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China
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Topcuoglu M, Aslan F. Evaluation of the Effect of a Novel β3-Adrenergic Agonist on Choroidal Vascularity. Invest Ophthalmol Vis Sci 2021; 62:17. [PMID: 34241623 PMCID: PMC8287045 DOI: 10.1167/iovs.62.9.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Purpose To determine the effect of the new β3-agonist (mirabegron), which is used for overactive bladder (OAB) treatment, on central retinal thickness (CRT) and choroidal vascularity. Material and Methods The 26 eyes of 26 cases using 50 mg tablet mirabegron once per day for OAB were included in this prospective case control study. The CRT, choroidal thickness (ChT), and choroidal vascularity were measured at baseline, week 1 (W1), month 1 (M1), month 2 (M2), and month 3 (M3). Subfoveal ChT measurement included the total subfoveal choroidal thickness (SFCT), and the small and large choroidal vessel layer (SCVL and LCVL) thickness. The total choroidal area (TCA), lumen area (LA), stromal area (SA), stroma/lumen ratio, and choroidal vascularity index (CVI) were measured with the Image-J software. Results The largest SFCT increase compared to baseline was at M1 (26.8 ± 40.8 µm, P = 0.001). The subfoveal SCVL thickness showed a significant decrease at M2 and M3 (−6.0 ± 8.9 µm, P = 0.002; −7.8 ± 13.4 µm, P = 0.046, respectively). LCVL thickness showed a significant increase at W1, M1, and M2, with the largest at M1. CVI showed a significant increase at M1, M2, and M3 (P < 0.05 for all). The TCA, LA, and SA showed a significant increasing trend at all follow-up periods. LA/SA decreased at W1 because of stromal expansion but increased at M3 with more prominent vascular dilatation. CRT values showed no significant change. Conclusions Mirabegron had a significant effect on choroidal thickness. Choroidal vascular response is in the form of narrowing in the choriocapillaris and enlargement in the Haller's layer.
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Affiliation(s)
- Murat Topcuoglu
- Alaaddin Keykubat University Education and Research Hospital, Department of Urology, Antalya, Turkey
| | - Fatih Aslan
- Alaaddin Keykubat University Education and Research Hospital, Department of Ophthalmology, Antalya, Turkey
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Selvaraj C, Selvaraj G, Mohamed Ismail R, Vijayakumar R, Baazeem A, Wei DQ, Singh SK. Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors. Saudi J Biol Sci 2021; 28:3650-3659. [PMID: 34220215 PMCID: PMC8241892 DOI: 10.1016/j.sjbs.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/25/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Bacillus anthracis is a gram positive, deadly spore forming bacteria causing anthrax and these bacteria having the complex mechanism in the cell wall envelope, which can adopt the changes in environmental conditions. In this, the membrane bound cell wall proteins are said to progressive drug target for the inhibition of Bacillus anthracis. Among the cell wall proteins, the SrtA is one of the important mechanistic protein, which mediate the ligation with LPXTG motif by forming the amide bonds. The SrtA plays the vital role in cell signalling, cell wall formation, and biofilm formations. Inhibition of SrtA leads to rupture of the cell wall and biofilm formation, and that leads to inhibition of Bacillus anthracis and thus, SrtA is core important enzyme to study the inhibition mechanism. In this study, we have examined 28 compounds, which have the inhibitory activity against the Bacillus anthracis SrtA for developing the 3D-QSAR and also, compounds binding selectivity with both open and closed SrtA conformations, obtained from 100 ns of MD simulations. The binding site loop deviate in forming the open and closed gate mechanism is investigated to understand the inhibitory profile of reported compounds, and results show the closed state active site conformations are required for ligand binding specificity. Overall, the present study may offer an opportunity for better understanding of the mechanism of action and can be aided to further designing of a novel and highly potent SrtA inhibitors.
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Affiliation(s)
- Chandrabose Selvaraj
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
| | - Gurudeeban Selvaraj
- Centre for Research in Molecular Modelling, Concordia University, 5618 Montreal, Quebec, Canada
| | - Randa Mohamed Ismail
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Department of Microbiology and Immunology, Veterinary Research Division, National Research Center (NRC), Giza, Egypt
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. QSAR Modeling, Molecular Docking and Molecular Dynamics Simulations Studies of Lysine-Specific Demethylase 1 (LSD1) Inhibitors as Anticancer Agents. Anticancer Agents Med Chem 2021; 21:987-1018. [PMID: 32698753 DOI: 10.2174/1871520620666200721134010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/07/2020] [Accepted: 05/17/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone Lysine Demetylases1 (LSD1) is a promising medication to treat cancer, which plays a crucial role in epigenetic modulation of gene expression. Inhibition of LSD1with small molecules has emerged as a vital mechanism to treat cancer. OBJECTIVE In the present research, molecular modeling investigations, such as CoMFA, CoMFA-RF, CoMSIA and HQSAR, molecular docking and Molecular Dynamics (MD) simulations were carried out on some tranylcypromine derivatives as LSD1 inhibitors. METHODS The QSAR models were carried out on a series of Tranylcypromine derivatives as data set via the SYBYL-X2.1.1 program. Molecular docking and MD simulations were carried out by the MOE software and the SYBYL program, respectively. The internal and external predictability performances related to the generated models for these LSD1 inhibitors were justified by evaluating cross-validated correlation coefficient (q2), noncross- validated correlation coefficient (r2ncv) and predicted correlation coefficient (r2pred) of the training and test set molecules, respectively. RESULTS The CoMFA (q2, 0.670; r2ncv, 0.930; r2pred, 0.968), CoMFA-RF (q2, 0.694; r2ncr, 0.926; r2pred, 0.927), CoMSIA (q2, 0.834; r2ncv, 0.956; r2pred, 0.958) and HQSAR models (q2, 0.854; r2ncv, 0.900; r2pred, 0.728) for training as well as the test set of LSD1 inhibition resulted in significant findings. CONCLUSION These QSAR models were found to be perfect and strong with better predictability. Contour maps of all models were generated and it was proven by molecular docking studies and molecular dynamics simulation that the hydrophobic, electrostatic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determining the structure-activity relationship. These theoretical results are possibly beneficial to design new strong LSD1 inhibitors with enhanced activity to treat cancer.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Esfandiar Heidarian
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
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10
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Structural investigation of isatin-based benzenesulfonamides as carbonic anhydrase isoform IX inhibitors endowed with anticancer activity using molecular modeling approaches. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Ghaleb A, Aouidate A, Ayouchia HBE, Aarjane M, Anane H, Stiriba SE. In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening. J Biomol Struct Dyn 2020; 40:143-153. [PMID: 32799761 DOI: 10.1080/07391102.2020.1808530] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q2= 0.54 and rext2=0.71. The molecular surflex-docking was applied to identify the crystal structure of CoV-2 main protease 3CLpro (PDB: 6LU7) and two potentially and largely used antiviral molecules, namely chloroquine, hydroxychloroquine. The obtained free energy affinity and ADMET properties indicate that among the series of model antiviral compounds examined, the new antiviral compound A5 could be an excellent antiviral drug inhibitor against COVID-19. The inhibition activity of pyridine N-oxyde compounds against CoV-2 was compared with the activity of two common antiviral drug, namely chloroquine (CQ) and hydroxychloroquine (HCQ). DFT method was also used to define the sites of reactivity of pyridine N-oxyde derivatives as well as CQ and HCQ.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adib Ghaleb
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Adnane Aouidate
- MCNSL, School of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Hicham Ben El Ayouchia
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Mohammed Aarjane
- LCBAE, Equipe Chimie Moléculaire et Molécules Bioactives, Université Moulay Ismail, Faculté des Sciences, Meknès, Morocco
| | - Hafid Anane
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Salah-Eddine Stiriba
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco.,Instituto de Ciencia Molecular/ICMol, Universidad de Valencia, Valencia, Spain
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12
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. Investigation of pyrimidine analogues as xanthine oxidase inhibitors to treat of hyperuricemia and gout through combined QSAR techniques, molecular docking and molecular dynamics simulations. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Xu Y, He Z, Liu H, Chen Y, Gao Y, Zhang S, Wang M, Lu X, Wang C, Zhao Z, Liu Y, Zhao J, Yu Y, Yang M. 3D-QSAR, molecular docking, and molecular dynamics simulation study of thieno[3,2- b]pyrrole-5-carboxamide derivatives as LSD1 inhibitors. RSC Adv 2020; 10:6927-6943. [PMID: 35493862 PMCID: PMC9049714 DOI: 10.1039/c9ra10085g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/01/2020] [Indexed: 12/28/2022] Open
Abstract
Histone Lysine Specific Demethylase 1 (LSD1) is overexpressed in many cancers and becomes a new target for anticancer drugs. In recent years, small molecule inhibitors with various structures targeting LSD1 have been reported. Here we report the binding interaction modes of a series of thieno[3,2-b]pyrrole-5-carboxamide LSD1 inhibitors using molecular docking, and three-dimensional quantitative structure-activity relationships (3D-QSAR). Comparative molecular field analysis (CoMFA q 2 = 0.783, r 2 = 0.944, r pred 2 = 0.851) and comparative molecular similarity indices analysis (CoMSIA q 2 = 0.728, r 2 = 0.982, r pred 2 = 0.814) were used to establish 3D-QSAR models, which had good verification and prediction capabilities. Based on the contour maps and the information of molecular docking, 8 novel small molecules were designed in silico, among which compounds D4, D5 and D8 with high predictive activity were subjected to further molecular dynamics simulations (MD), and their possible binding modes were explored. It was found that Asn535 plays a crucial role in stabilizing the inhibitors. Furthermore, ADME and bioavailability prediction for D4, D5 and D8 were carried out. The results would provide valuable guidance for designing new reversible LSD1 inhibitors in the future.
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Affiliation(s)
- Yongtao Xu
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Zihao He
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Hongyi Liu
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Yifan Chen
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Yunlong Gao
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Songjie Zhang
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Meiting Wang
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
| | - Xiaoyuan Lu
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Chang Wang
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Zongya Zhao
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Yan Liu
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Junqiang Zhao
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Yi Yu
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
| | - Min Yang
- School of Biomedical Engineering, Xinxiang Medical University Xinxiang Henan 453003 China
- Xinxiang Key Laboratory of Biomedical Information Research Xinxiang Henan 453003 China
- Henan Engineering Laboratory of Combinatorial Technique for Clinical and Biomedical Big Data Xinxiang Henan 453003 China
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In silico studies of novel scaffold of thiazolidin-4-one derivatives as anti-Toxoplasma gondii agents by 2D/3D-QSAR, molecular docking, and molecular dynamics simulations. Struct Chem 2020. [DOI: 10.1007/s11224-019-01458-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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15
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QSAR analysis of coumarin-based benzamides as histone deacetylase inhibitors using CoMFA, CoMSIA and HQSAR methods. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.126961] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Lorca M, Valdes Y, Chung H, Romero-Parra J, Pessoa-Mahana CD, Mella J. Three-Dimensional Quantitative Structure-Activity Relationships (3D-QSAR) on a Series of Piperazine-Carboxamides Fatty Acid Amide Hydrolase (FAAH) Inhibitors as a Useful Tool for the Design of New Cannabinoid Ligands. Int J Mol Sci 2019; 20:ijms20102510. [PMID: 31117309 PMCID: PMC6566251 DOI: 10.3390/ijms20102510] [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: 02/21/2019] [Revised: 04/27/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022] Open
Abstract
Fatty Acid Amide Hydrolase (FAAH) is one of the main enzymes responsible for endocannabinoid metabolism. Inhibition of FAAH increases endogenous levels of fatty acid ethanolamides such as anandamide (AEA) and thus consitutes an indirect strategy that can be used to modulate endocannabinoid tone. In the present work, we present a three-dimensional quantitative structure-activity relationships/comparative molecular similarity indices analysis (3D-QSAR/CoMSIA) study on a series of 90 reported irreversible inhibitors of FAAH sharing a piperazine-carboxamide scaffold. The model obtained was extensively validated (q2 = 0.734; r2 = 0.966; r2m = 0.723). Finally, based on the information derived from the contour maps we designed a series of 10 new compounds with high predicted FAAH inhibition (predicted pIC50 of the best-proposed compounds = 12.196; 12.416).
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Affiliation(s)
- Marcos Lorca
- Escuela de Quimica y Farmacia, Facultad de Medicina, Universidad Andres Bello, Quillota 980, Viña del Mar 2531015, Chile.
| | - Yudisladys Valdes
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Hery Chung
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Javier Romero-Parra
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta 1270709, Chile.
| | - C David Pessoa-Mahana
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Jaime Mella
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile.
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Santa Marta 183, Valparaíso 2360134, Chile.
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17
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Zhang G, Ren Y. Molecular Modeling and Design Studies of Purine Derivatives as Novel CDK2 Inhibitors. Molecules 2018; 23:molecules23112924. [PMID: 30423939 PMCID: PMC6278423 DOI: 10.3390/molecules23112924] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential target for treating cancer. Purine heterocycles have attracted particular attention as the scaffolds for the development of CDK2 inhibitors. To explore the interaction mechanism and the structure–activity relationship (SAR) and to design novel candidate compounds as potential CDK2 inhibitors, a systematic molecular modeling study was conducted on 35 purine derivatives as CDK2 inhibitors by combining three-dimensional quantitative SAR (3D-QSAR), virtual screening, molecular docking, and molecular dynamics (MD) simulations. The predictive CoMFA model (q2 = 0.743, rpred2 = 0.991), the CoMSIA model (q2 = 0.808, rpred2 = 0.990), and the Topomer CoMFA model (q2 = 0.779, rpred2 = 0.962) were obtained. Contour maps revealed that the electrostatic, hydrophobic, hydrogen bond donor and steric fields played key roles in the QSAR models. Thirty-one novel candidate compounds with suitable predicted activity (predicted pIC50 > 8) were designed by using the results of virtual screening. Molecular docking indicated that residues Asp86, Glu81, Leu83, Lys89, Lys33, and Gln131 formed hydrogen bonds with the ligand, which affected activity of the ligand. Based on the QSAR model prediction and molecular docking, two candidate compounds, I13 and I60 (predicted pIC50 > 8, docking score > 10), with the most potential research value were further screened out. MD simulations of the corresponding complexes of these two candidate compounds further verified their stability. This study provided valuable information for the development of new potential CDK2 inhibitors.
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Affiliation(s)
- Gaomin Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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