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Saleem M, Mazhar Fareed M, Salman Akbar Saani M, Shityakov S. Network pharmacology and multitarget analysis of Nigella sativa in the management of diabetes and obesity: a computational study. J Biomol Struct Dyn 2024; 42:4800-4816. [PMID: 37350443 DOI: 10.1080/07391102.2023.2222837] [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: 02/02/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Obesity and diabetes are commonly associated with one another and represent a significant global health issue, with a recent surge in disease incidence. Nigella sativa, also known as black cumin, is believed to possess several health benefits, including anti-diabetic, anticancer, antioxidant, antimicrobial, and anti-obesity properties. In this study, we aimed to identify the active compounds derived from N. sativa, which can potentially inhibit key protein targets and signaling pathways associated with diabesity treatment. We employed an exhaustive in silico search, which led to the identification of 22 potential compounds. Out of these, only five hits were found to be non-toxic, including Arabic and ascorbic acids, dihydrocodeine, catechin, and kaempferol. Our analysis revealed that these hits were associated with genes such as AKT1, IL6, SRC, and EGFR. Finally, we conducted molecular docking and molecular dynamics simulations, which identified kaempferol as the best binder for AKT1 in comparison to the reference molecule. Overall, our in silico integrated pipeline provides a useful approach to identify non-toxic phytocompounds as promising drug candidates to treat diabetes and obesity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muntaha Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Mazhar Fareed
- Department of Computer Science, School of Science and Engineering, Università degli studi di Verona, Verona, Italy
- Department of Biotechnology, Applied Bioinformatics Group, Università degli studi di Verona, Verona, Italy
| | | | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russian Federation
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2
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Onikanni SA, Lawal B, Fadaka AO, Bakare O, Adewole E, Taher M, Khotib J, Susanti D, Oyinloye BE, Ajiboye BO, Ojo OA, Sibuyi NRS. Computational and Preclinical Prediction of the Antimicrobial Properties of an Agent Isolated from Monodora myristica: A Novel DNA Gyrase Inhibitor. Molecules 2023; 28:molecules28041593. [PMID: 36838579 PMCID: PMC9966190 DOI: 10.3390/molecules28041593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
The African nutmeg (Monodora myristica) is a medically useful plant. We, herein, aimed to critically examine whether bioactive compounds identified in the extracted oil of Monodora myristica could act as antimicrobial agents. To this end, we employed the Schrödinger platform as the computational tool to screen bioactive compounds identified in the oil of Monodora myristica. Our lead compound displayed the highest potency when compared with levofloxacin based on its binding affinity. The hit molecule was further subjected to an Absorption, Distribution, Metabolism, Excretion (ADME) prediction, and a Molecular Dynamics (MD) simulation was carried out on molecules with PubChem IDs 529885 and 175002 and on three standards (levofloxacin, cephalexin, and novobiocin). The MD analysis results demonstrated that two molecules are highly compact when compared to the native protein; thereby, this suggests that they could affect the protein on a structural and a functional level. The employed computational approach demonstrates that conformational changes occur in DNA gyrase after the binding of inhibitors; thereby, this resulted in structural and functional changes. These findings expand our knowledge on the inhibition of bacterial DNA gyrase and could pave the way for the discovery of new drugs for the treatment of multi-resistant bacterial infections.
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Affiliation(s)
- Sunday Amos Onikanni
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Biochemistry Unit, Department of Chemical Sciences, Afe Babalola University, Ado-Ekiti 360101, Nigeria
- Correspondence: or (S.A.O.); (J.K.); (B.O.A.)
| | - Bashir Lawal
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | - Oluwafemi Bakare
- Department of Biochemistry, Faculty of Science, Adekunle Ajasin University, Akungba Akoko 342111, Nigeria
| | - Ezekiel Adewole
- Industrial Chemistry Unit, Department of Chemical Sciences, Afe Babalola University, Ado-Ekiti 360101, Nigeria
| | - Muhammad Taher
- Department of Pharmaceutical Technology, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
- Pharmaceutics and Translational Research Group, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - Junaidi Khotib
- Department of Pharmacy Practice, Faculty of Pharmacy, Airlangga University, Surabaya 60115, Indonesia
- Correspondence: or (S.A.O.); (J.K.); (B.O.A.)
| | - Deny Susanti
- Department of Chemistry, Kulliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - Babatunji Emmanuel Oyinloye
- Biochemistry Unit, Department of Chemical Sciences, Afe Babalola University, Ado-Ekiti 360101, Nigeria
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, Kwadlangezwa 3886, South Africa
- Institute of Drug Research and Development, SE Bogoro Center, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria
| | - Basiru Olaitan Ajiboye
- Institute of Drug Research and Development, SE Bogoro Center, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria
- Phytomedicine and Molecular Toxicology Research Laboratory, Department of Biochemistry, Federal University Oye-Ekiti, Oye-Ekiti 371104, Nigeria
- Correspondence: or (S.A.O.); (J.K.); (B.O.A.)
| | - Oluwafemi Adeleke Ojo
- Phytomedicine, Molecular Toxicology, and Computational Biochemistry Research Laboratory (PMTCB-RL), Department of Biochemistry, Bowen University, Iwo 232101, Nigeria
| | - Nicole Remaliah Samantha Sibuyi
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
- Health Platform, Advanced Materials Division, Mintek, Randburg 2194, South Africa
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Integrating Network Pharmacology and Molecular Docking Approaches to Decipher the Multi-Target Pharmacological Mechanism of Abrus precatorius L. Acting on Diabetes. Pharmaceuticals (Basel) 2022; 15:ph15040414. [PMID: 35455411 PMCID: PMC9029140 DOI: 10.3390/ph15040414] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a notable health care load that imposes a serious impact on the quality of life of patients. The small amount of reported data and multiple spectra of pathophysiological mechanisms of T2DM make it a challenging task and serious economic burden in health care management. Abrus precatorius L. is a slender, perennial, deciduous, and woody twining plant used in various regions of Asia to treat a variety of ailments, including diabetes mellitus. Various in vitro studies revealed the therapeutic significance of A. precatorius against diabetes. However, the exact molecular mechanism remains unclarified. In the present study, a network pharmacology technique was employed to uncover the active ingredients, their potential targets, and signaling pathways in A. precatorius for the treatment of T2DM. In the framework of this study, we explored the active ingredient–target–pathway network and figured out that abrectorin, abrusin, abrisapogenol J, sophoradiol, cholanoic acid, precatorine, and cycloartenol decisively contributed to the development of T2DM by affecting AKT1, MAPK3, TNFalpha, and MAPK1 genes. Later, molecular docking was employed to validate the successful activity of the active compounds against potential targets. Lastly, we conclude that four highly active constituents, namely, abrusin, abrisapogenol J, precatorine, and cycloartenol, help in improving the body’s sensitivity to insulin and regulate the expression of AKT1, MAPK3, TNFalpha, and MAPK1, which may act as potential therapeutic targets of T2DM. Integrated network pharmacology and docking analysis revealed that A. precatorius exerted a promising preventive effect on T2DM by acting on diabetes-associated signaling pathways. This provides a basis to understand the mechanism of the anti-diabetes activity of A. precatorius.
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Wang X, Fan Y, Xu F, Xie J, Gao X, Li L, Tian Y, Sheng J. Characterization of the structure, stability, and activity of hypoglycemic peptides from Moringa oleifera seed protein hydrolysates. Food Funct 2022; 13:3481-3494. [PMID: 35246675 DOI: 10.1039/d1fo03413h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Moringa oleifera seed protein hydrolysates exhibit good hypoglycemic activity, but their specific peptide components have not yet been characterized. Here, we identified the ultrafiltration peptide components (<3 kDa) of M. oleifera seed protein hydrolysates. A highly active α-glucosidase inhibitory peptide with an IC50 value of 109.65 μM (MoHpP-2) with the amino acid sequence KETTTIVR was identified. We characterized its structural properties, stability, and hypoglycemic activity. MoHpP-2 was found to be an amphipathic peptide with a β-turn structure, and the hemolysis of red blood cells was not observed when its concentration was lower than 2 mg mL-1. MoHpP-2 was stable under weakly acidic conditions, at temperatures lower than 60 °C, and at high ion concentrations. Western blotting revealed that MoHpP-2 affected the PI3K and AMPK pathways of HepG2 cells. Molecular docking revealed that MoHpP-2 interacted with α-glucosidase through hydrogen bonding and hydrophobic forces. Thus, MoHpP-2 from M. oleifera seeds could be used to make hypoglycemic functional foods.
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Affiliation(s)
- Xuefeng Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Yaozhu Fan
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Feiran Xu
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P. R. China
| | - Jing Xie
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Xiaoyu Gao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Lingfei Li
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, P. R. China. .,Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, National Research and Development Professional Center for Moringa Processing Technology, Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, 650201, P. R. China
| | - Jun Sheng
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, P. R. China.
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Fadaka AO, Sibuyi NRS, Madiehe AM, Meyer M. Computational insight of dexamethasone against potential targets of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:875-885. [PMID: 32924825 PMCID: PMC7544935 DOI: 10.1080/07391102.2020.1819880] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
The health sector has been on the race to find a potent therapy for coronavirus disease (COVID)-19, a diseases caused by severe acute respiratory syndrome coronavirus (SARS-CoV)-2. Repurposed anti-viral drugs have played a huge role in combating the virus, and most recently, dexamethasone (Dex) have shown its therapeutic activity in severe cases of COVID-19 patients. The study sought to provide insights on the anti-COVID-19 mechanism of Dex at both atomic and molecular level against SARS-CoV-2 targets. Computational methods were employed to predict the binding affinity of Dex to SARS-CoV-2 using the Schrodinger suite (v2020-2). The target molecules and ligand (Dex) were retrieved from PDB and PubChem, respectively. The selected targets were SARS-CoV-2 main protease (Mpro), and host secreted molecules glucocorticoid receptor, and Interleukin-6 (IL-6). Critical analyses such as Protein and ligand preparation, molecular docking, molecular dynamic (MD) simulations, and absorption, distribution, metabolism, excretion (ADME), and toxicity analyses were performed using the targets and the ligand as inputs. Dex showed stronger affinity to its theoretical (glucocorticoid) receptor with a superior docking score of -14.7 and a good binding energy value of -147.48 kcal/mol; while short hydrogen bond distances were observed in both Mpro and IL-6 when compared to glucocorticoid receptor. Based on these findings, Dex-target complexes were used to perform MD simulations to analyze Dex stability at 50 ns. This study demonstrates that Dex could bind to both the viral and host receptors as a potential drug candidate for COVID-19. To ascertain the biological fitness of this study, other SARS-CoV-2 targets should be explored. Also, the in vitro studies of dexamethasone against several SARS-CoV-2 targets warrant further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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6
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Hasib RA, Ali MC, Rahman MS, Rahman MM, Ahmed FF, Mashud MAA, Islam MA, Jamal MAHM. A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds. F1000Res 2021. [DOI: 10.12688/f1000research.73999.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.
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7
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Sahin K, Saripinar E, Durdagi S. Combined 4D-QSAR and target-based approaches for the determination of bioactive Isatin derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:769-792. [PMID: 34530651 DOI: 10.1080/1062936x.2021.1971760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The hybrid method of the Electron-Conformational Genetic Algorithm (EC-GA) was used to determine the pharmacophore groups and to estimate anticancer activity in isatin derivatives using a robust 4D-QSAR software (EMRE). To build the model, each compound is represented by a set of conformers rather than a single conformation. The Electron Conformational Matrix of Congruity (ECMC) is composed via EMRE software. Electron Conformational Submatrix of Activity (ECSA) was calculated by the comparison of these matrices. Genetic algorithm was used to select important variables to predict theoretical activity. The model with the best seven parameters produced satisfactory results. The E statistics technique was applied to the generated EC-GA model to evaluate the individual contribution of each of the descriptors on biological activity. The r2 and q2 values of the training set compounds were found to be 0.95 and 0.93, respectively. Because no previous 4D-QSAR studies on isatin derivatives have been conducted, this study is important in the development of new isatin derivatives. In this study, 27 isatin derivatives whose activities were estimated using the hybrid EC-GA method were also investigated through molecular docking and molecular dynamics simulations for their BCL-2 inhibitory activity.
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Affiliation(s)
- K Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - E Saripinar
- Faculty of Science, Department of Chemistry, Erciyes University, Kayseri, Turkey
| | - S Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Ru X, Ye X, Sakurai T, Zou Q, Xu L, Lin C. Current status and future prospects of drug-target interaction prediction. Brief Funct Genomics 2021; 20:312-322. [PMID: 34189559 DOI: 10.1093/bfgp/elab031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/09/2023] Open
Abstract
Drug-target interaction prediction is important for drug development and drug repurposing. Many computational methods have been proposed for drug-target interaction prediction due to their potential to the time and cost reduction. In this review, we introduce the molecular docking and machine learning-based methods, which have been widely applied to drug-target interaction prediction. Particularly, machine learning-based methods are divided into different types according to the data processing form and task type. For each type of method, we provide a specific description and propose some solutions to improve its capability. The knowledge of heterogeneous network and learning to rank are also summarized in this review. As far as we know, this is the first comprehensive review that summarizes the knowledge of heterogeneous network and learning to rank in the drug-target interaction prediction. Moreover, we propose three aspects that can be explored in depth for future research.
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Affiliation(s)
| | - Xiucai Ye
- Department of Computer Science, and Center for Artificial Intelligence Research (C-AIR), University of Tsukuba
| | - Tetsuya Sakurai
- Department of Computer Science and is the director of the C-AIR, University of Tsukuba
| | - Quan Zou
- University of Electronic Science and Technology of China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic
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9
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Zhai T, Zhang F, Haider S, Kraut D, Huang Z. An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease. Front Mol Biosci 2021; 8:661424. [PMID: 34079818 PMCID: PMC8166273 DOI: 10.3389/fmolb.2021.661424] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
The newly evolved SARS-CoV-2 has caused the COVID-19 pandemic, and the SARS-CoV-2 main protease 3CLpro is essential for the rapid replication of the virus. Inhibiting this protease may open an alternative avenue toward therapeutic intervention. In this work, a computational docking approach was developed to identify potential small-molecule inhibitors for SARS-CoV-2 3CLpro. Totally 288 potential hits were identified from a half-million bioactive chemicals via a protein-ligand docking protocol. To further evaluate the docking results, a quantitative structure activity relationship (QSAR) model of 3CLpro inhibitors was developed based on existing small molecule inhibitors of the 3CLproSARS- CoV- 1 and their corresponding IC50 data. The QSAR model assesses the physicochemical properties of identified compounds and estimates their inhibitory effects on 3CLproSARS- CoV- 2. Seventy-one potential inhibitors of 3CLpro were selected through these computational approaches and further evaluated via an enzyme activity assay. The results show that two chemicals, i.e., 5-((1-([1,1'-biphenyl]-4-yl)-2,5-dimethyl-1H-pyrrol-3-yl)methylene)pyrimidine-2,4,6(1H,3H,5H)-trione and N-(4-((3-(4-chlorophenylsulfonamido)quinoxalin-2-yl)amino)phenyl)acetamide, effectively inhibited 3CLpro SARS-CoV-2 with IC50's of 19 ± 3 μM and 38 ± 3 μM, respectively. The compounds contain two basic structures, pyrimidinetrione and quinoxaline, which were newly found in 3CLpro inhibitor structures and are of high interest for lead optimization. The findings from this work, such as 3CLpro inhibitor candidates and the QSAR model, will be helpful to accelerate the discovery of inhibitors for related coronaviruses that may carry proteases with similar structures to SARS-CoV-2 3CLpro.
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Affiliation(s)
- Tianhua Zhai
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA, United States
| | - Fangyuan Zhang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA, United States
| | - Shozeb Haider
- School of Pharmacy, University College London (UCL), London, United Kingdom
| | - Daniel Kraut
- Department of Chemistry, Villanova University, Villanova, PA, United States
| | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA, United States
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10
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Sahin K, Orhan MD, Avsar T, Durdagi S. Hybrid In Silico and TR-FRET-Guided Discovery of Novel BCL-2 Inhibitors. ACS Pharmacol Transl Sci 2021; 4:1111-1123. [PMID: 34151203 DOI: 10.1021/acsptsci.0c00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/31/2022]
Abstract
B-Cell lymphoma 2 (BCL-2) regulates cell death in humans. In this study, combined multiscale in silico approaches and in vitro studies were employed. A small-molecule library that includes more than 210 000 compounds was used. The predicted therapeutic activity value (TAV) of the compounds in this library was computed with the binary cancer quantitative structure-activity relationships (QSAR) model. The molecules with a high calculated TAV were used in 26 individual toxicity QSAR models. As a result of this screening protocol, 288 nontoxic molecules with high predicted TAV were identified. These selected hits were then screened against the BCL-2 target protein using hybrid docking and molecular dynamics (MD) simulations. The interaction energies of identified compounds were compared with two known BCL-2 inhibitors. Then, the short MD simulations were carried out by initiating the best docking poses of 288 molecules. Average MM/GBSA energies were computed, and long MD simulations were employed to selected hits. The same calculations were also applied for two known BCL-2 inhibitors. Moreover, a five-site (AHRRR) structure-based pharmacophore model was constructed, and this model was used in the screening of the same database. On the basis of hybrid data-driven ligand identification study, final hits were selected and used in in vitro studies. Based on results of the time-resolved fluorescence resonance energy transfer (TR-FRET) analysis, further filtration was carried out for the U87-MG cell line tests. MTT cell proliferation assay analysis results showed that selected three potent compounds were significantly effective on glioma cells.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey
| | - Timucin Avsar
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Virtual Drug Screening and Development Laboratory, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
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11
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Ma S, McGann M, Enyedy IJ. The influence of calculated physicochemical properties of compounds on their ADMET profiles. Bioorg Med Chem Lett 2021; 36:127825. [PMID: 33508464 DOI: 10.1016/j.bmcl.2021.127825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022]
Abstract
We analyzed the influence of calculated physicochemical properties of more than 20,000 compounds on their P-gp and BCRP mediated efflux, microsomal stability, hERG inhibition, and plasma protein binding. Our goal was to provide guidance for designing compounds with desired pharmacokinetic profiles. Our analysis showed that compounds with ClogP less than 3 and molecular weight less than 400 will have high microsomal stability and low plasma protein binding. Compounds with logD less than 2.2 and/or basic pKa larger than 5.3 are likely to be BCRP substrates and compounds with basic pKa less than 5.2 and/or acidic pKa less than 13.4 are less likely to inhibit hERG. Based on these results, compounds with MW < 400, ClogP < 3, basic pKa < 5.2 and acidic pKa < 13.4 are likely to have good bioavailability and low hERG inhibition.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/chemistry
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- ATP Binding Cassette Transporter, Subfamily G, Member 2/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism
- Animals
- Blood Proteins/chemistry
- Blood Proteins/metabolism
- Chemistry, Physical
- Dose-Response Relationship, Drug
- Ether-A-Go-Go Potassium Channels/antagonists & inhibitors
- Ether-A-Go-Go Potassium Channels/genetics
- Ether-A-Go-Go Potassium Channels/metabolism
- Humans
- Mice
- Microsomes/chemistry
- Microsomes/metabolism
- Molecular Structure
- Molecular Weight
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/metabolism
- Pharmaceutical Preparations/chemistry
- Rats
- Structure-Activity Relationship
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Affiliation(s)
- Shifan Ma
- Medicinal Chemistry, Biotherapeutic and Medicinal Science Department, Biogen, 225 Binney Street, Cambridge, MA 02142, United States
| | - Mark McGann
- OpenEye Scientific, Santa Fe, NM 87507, United States
| | - Istvan J Enyedy
- Medicinal Chemistry, Biotherapeutic and Medicinal Science Department, Biogen, 225 Binney Street, Cambridge, MA 02142, United States.
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12
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Aventurado CA, Billones JB, Vasquez RD, Castillo AL. In Ovo and In Silico Evaluation of the Anti-Angiogenic Potential of Syringin. Drug Des Devel Ther 2020; 14:5189-5204. [PMID: 33268982 PMCID: PMC7701684 DOI: 10.2147/dddt.s271952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Cancer is considered as one of the deadliest human diseases today. Angiogenesis, the propagation of new blood vessels from pre-existing vasculature, is a critical step in the progression of cancer as it is essential in the growth and metastasis of tumors. Hence, suppression of angiogenesis is a promising approach in cancer therapy. Syringin, a phenylpropanoid glycoside with a molecular formula of C17H24O9, has been found to exhibit chemopreventive effects. However, its anti-angiogenic activity and the underlying mechanism of action are still unknown. METHODS In this work, in ovo chorioallantoic membrane (CAM) assay has been conducted to evaluate the effect of syringin on neovascularization. Additionally, reverse molecular docking studies have been performed in order to identify the probable enzyme targets in the angiogenesis pathway. RESULTS Treatment with syringin showed significant dose-dependent inhibition of blood vessel length and junctions in the CAM of duck eggs; the anti-angiogenic activity of syringin at 100 µM and 200 µM is comparable with 200 µM of the positive control celecoxib. The results of reverse docking studies indicate that syringin binds the strongest to dihydrofolate reductase (DHFR) and, to some extent, with transforming growth factor-beta receptor type 1 (TGF-βR1), vascular endothelial growth factor receptor 2 (VEGFR2), and matrix metalloproteinase-2 (MMP-2). Furthermore, ADMET models revealed that syringin potentially possesses excellent pharmacokinetic and toxicity profiles. CONCLUSION This study demonstrates the potential of syringin as an anti-angiogenic agent and elicits further investigations to establish its application in cancer suppression.
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Affiliation(s)
| | - Junie B Billones
- Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila, Philippines
| | - Ross D Vasquez
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
| | - Agnes L Castillo
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
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13
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Sahin K. In silico identification of angiotensin-1 converting enzyme inhibitors using text mining and virtual screening. J Biomol Struct Dyn 2020; 40:1152-1162. [PMID: 33016840 DOI: 10.1080/07391102.2020.1827038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cardiovascular diseases are the world's leading cause of death. Hypertension is an important risk factor for cardiovascular and renal diseases. Angiotensin-converting enzyme (ACE) can be a possible therapeutic target for managing angiotensin I conversion to angiotensin II and ultimately controlling hypertension. Indole is an significant fragment used in many medicines approved by FDA. For this reason, the molecules in their fragments containing" indol" keywords were taken from the Specs-SC (small compound) database. The predicted therapeutc activity values (TAV) of these compounds against hypertension were evaluated using binary models of QSAR by MetaCore/MetaDrug. For the 26 separate QSAR models of toxicity, molecules with measured TAV greater than 0.5 were used. 3792 non-toxic compounds were investigated by molecular docking study and molecular dynamics simulations for their ACE inhibitory activity. Glide standard precision (SP) of Maestro Molecular Modeling pocket was used to perform molecular docking. Short molecular dynamics (MD) simulations (5-ns) were carried out by initiating the top docking poses of selected 40 molecules. To quantitatively evaluate the predicted binding affinity of a screened compound, average MM/GBSA scores of screened ligands were calculated and based on their binding free energy values, hit compounds were identified for the long (100-ns) MD simulations. Root mean square deviation and root mean square fluctuations were also calculated to assess the structural characteristics and observe fluctuations of the 100-ns time scale. Thus, with the application of text mining and integrated molecular modeling we reported novel indole-based hit inhibitors for ACE-1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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14
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Sahin K. Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining. J Biomol Struct Dyn 2020; 39:3638-3648. [PMID: 32496942 DOI: 10.1080/07391102.2020.1775121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) inhibitors have been used as possible therapeutic agents for HIV-1 infection in clinical study. Most of the HIV therapy-related problems usually stem from long-term opioid usage. The rapid development of drug-resistant variants limits the long-term effectiveness of current inhibitors as therapeutic agents. In addition, different side effects were reported. Further drug development is required to design new compounds which have similar efficacy as the drugs currently used in HIV infection but without having undesirable side effects. Indole derivatives were considered as one of the effective HIV inhibitors. Indole is an important fragment used in many FDAapproved medicines and used in various diseases. For this purpose, in this study the molecules containing" indole" keywords in their fragments are taken from the Specs-SC database which includes 212520 small molecules. 5194 molecules that include indole keywords are selected. These selected molecules are then screened against HIV-1 PR target protein using molecular docking simulations. Then the molecules are ranked according to the their docking scores. Top docking poses of ten ligands and FDA approved drug Amprenavir are subjected to 100 ns Molecular Dynamics (MD) simulations. Thus, by using combination of text mining and integrated molecular modeling approaches, we identified novel indole-based hits against HIV-1 PR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Şahİn K, DurdaĞi S. Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors. Turk J Chem 2020; 44:574-588. [PMID: 33488178 PMCID: PMC7671205 DOI: 10.3906/kim-1911-57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/03/2020] [Indexed: 11/26/2022] Open
Abstract
The excessive activity of acetylcholinesterase enzyme (AChE) causes different neuronal problems, especially dementia and neuronal cell deaths. Food and Drug Administration (FDA) approved drugs donepezil, rivastigmine, tacrine and galantamine are AChE inhibitors and in the treatment of Alzheimer’s disease (AD) these drugs are currently prescribed. However, these inhibitors have various adverse side effects. Therefore, there is a great need for the novel selective AChE inhibitors with fewer adverse side effects for the effective treatment. In this study, combined ligand-based and structure-based virtual screening approaches were used to identify new hit compounds from small molecules library of National Cancer Institute (NCI) containing approximately 265,000 small molecules. In the present study, we developed a computational pipeline method to predict the binding affinities of the studied compounds at the specific target sites. For this purpose, a text mining study was carried out initially and compounds containing the keyword “indol” were considered. The therapeutic activity values against AD were screened using the binary quantitative structure activity relationship (QSAR) models. We then performed docking, molecular dynamics (MD) simulations and free energy analysis to clarify the interactions between selected ligands and enzyme. Thus, in this study we identified new promising hit compounds from a large database that may be used to inhibit the enzyme activity of AChE.
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Affiliation(s)
- Kader Şahİn
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
| | - Serdar DurdaĞi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
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16
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SAHİN K, DURDAGI S. Identifying the Novel Pyrimidine-Based CDK2 Inhibitors as Anticancer Agents Using Text-Mining and Combined Molecular Modeling Approaches. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2020. [DOI: 10.18596/jotcsa.701243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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17
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Iraji A, Khoshneviszadeh M, Firuzi O, Khoshneviszadeh M, Edraki N. Novel small molecule therapeutic agents for Alzheimer disease: Focusing on BACE1 and multi-target directed ligands. Bioorg Chem 2020; 97:103649. [PMID: 32101780 DOI: 10.1016/j.bioorg.2020.103649] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/05/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that effects 50 million people worldwide. In this review, AD pathology and the development of novel therapeutic agents targeting AD were fully discussed. In particular, common approaches to prevent Aβ production and/or accumulation in the brain including α-secretase activators, specific γ-secretase modulators and small molecules BACE1 inhibitors were reviewed. Additionally, natural-origin bioactive compounds that provide AD therapeutic advances have been introduced. Considering AD is a multifactorial disease, the therapeutic potential of diverse multi target-directed ligands (MTDLs) that combine the efficacy of cholinesterase (ChE) inhibitors, MAO (monoamine oxidase) inhibitors, BACE1 inhibitors, phosphodiesterase 4D (PDE4D) inhibitors, for the treatment of AD are also reviewed. This article also highlights descriptions on the regulator of serotonin receptor (5-HT), metal chelators, anti-aggregants, antioxidants and neuroprotective agents targeting AD. Finally, current computational methods for evaluating the structure-activity relationships (SAR) and virtual screening (VS) of AD drugs are discussed and evaluated.
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Affiliation(s)
- Aida Iraji
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsima Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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18
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Sahin K, Zengin Kurt B, Sonmez F, Durdagi S. Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays. J Biomol Struct Dyn 2019; 38:3342-3358. [PMID: 31462153 DOI: 10.1080/07391102.2019.1660218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the current work, we developed a computational pipeline method for predicting the binding affinities of studied compounds at the specific target sites. Since many approved therapeutic compounds involve indole or indole-derivative rings, in the current study we focused compounds including these fingerprints. Initially, 212520 compounds were retrieved from Specs-SC library and after the conversion of IUPAC text file format, compounds that include 'indol' keyword (5194 compounds) were used in binary QSAR-based models to screen against a defined therapeutic activity "Alzheimer's disease" (AD). The molecules that have higher AD therapeutic activity values (>0.5) were then used in the 26 different toxicity-QSAR models. Binary QSAR models resulted 89 hits that have high AD therapeutic activity and no toxicity. Selected 89 molecules were then screened against acetylcholinesterase (AChE) targets using molecular docking and top-docking poses of compounds were used in initially short (10 ns) molecular dynamics (MD) simulations. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were performed for 89 ligands and tightly bound 17 ligands based on average MM/GBSA scores were selected for long (100 ns) MD simulations. The same protocol was also applied for the known 4 AChE inhibitors. Selected hits were also docked to the binding pocket of butyrylcholinesterase (BChE). Finally, based on MM/GBSA scores, as well as their corresponding docking scores and metabolite production profiles, 7 compounds were selected and their in vitro tests were performed. Out of 7 compounds, 6 of them showed μM-level inhibition for both AChE and BChE targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Belma Zengin Kurt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, Turkey
| | - Fatih Sonmez
- Pamukova Vocational High School, Sakarya University of Applied Sciences, Sakarya, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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19
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Yang B, Mao J, Gao B, Lu X. Computer-Assisted Drug Virtual Screening Based on the Natural Product Databases. Curr Pharm Biotechnol 2019; 20:293-301. [PMID: 30919773 DOI: 10.2174/1389201020666190328115411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/20/2018] [Accepted: 03/08/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Computer-assisted drug virtual screening models the process of drug screening through computer simulation technology, by docking small molecules in some of the databases to a certain protein target. There are many kinds of small molecules databases available for drug screening, including natural product databases. METHODS Plants have been used as a source of medication for millennia. About 80% of drugs were either natural products or related analogues by 1990, and many natural products are biologically active and have favorable absorption, distribution, metabolization, excretion, and toxicology. RESULTS In this paper, we review the natural product databases' contributions to drug discovery based on virtual screening, focusing particularly on the introductions of plant natural products, microorganism natural product, Traditional Chinese medicine databases, as well as natural product toxicity prediction databases. CONCLUSION We highlight the applications of these databases in many fields of virtual screening, and attempt to forecast the importance of the natural product database in next-generation drug discovery.
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Affiliation(s)
- Baoyu Yang
- Department of Biochemistry and Cell Biology, The School of Life Science, Liaoning University, Shenyang 110036, China
| | - Jing Mao
- Department of Biochemistry and Cell Biology, The School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bing Gao
- Department of Cell Biology and Genetics, Shenyang Medical College, 146 Huanghe North Street, Shenyang 110034, China
| | - Xiuli Lu
- Department of Biochemistry and Cell Biology, The School of Life Science, Liaoning University, Shenyang 110036, China
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20
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Shakil S. Molecular interaction of investigational ligands with human brain acetylcholinesterase. J Cell Biochem 2019; 120:11820-11830. [PMID: 30746750 DOI: 10.1002/jcb.28461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/09/2018] [Accepted: 12/13/2018] [Indexed: 01/24/2023]
Abstract
Alzheimer's disease, a neurodegenerative disorder continues to be an area of investigation by the international researchers' fraternity. Despite all the ongoing efforts, the effective set of promising cholinesterase inhibitors available in the market for patients' use is limited. Furthermore, the currently available drugs could provide only a palliative type of treatment instead of providing a complete cure or foolproof prevention. Hence, design/discovery of fresh drug molecules as acetylcholinesterase (AChE) inhibitors still remains an urgent requirement. The drug discovery platform, MCULE in the "structure-based virtual screening" (SBVS) mode was used for high throughput ligand screening of over five million structures targeted against the AChE catalytic site. A stepwise query was made for the SBVS input. The number of hits was narrowed down in consecutive succession via varied filtration criteria as AutoDock-Vina rankings, MCULE toxicity filtration, exclusion of ligands having less than four H-bond acceptors, filtration by ΔG cutoff, rule-of-five violation and SWISS ADME profiling. This was followed by holistic analysis of all the results, thereby leading to one promising ligand. The screened out drug molecule, MCULE-5872671137-0-1 exhibited a robust interaction with the AChE catalytic site involving 20 amino acid residues, an acceptable binding free energy of -10.2 kcal/mol in addition to a favorable SWISS ADME-profie showing no harmful effects on the human body. It can be carefully stated that the molecule, MCULE-5872671137-0-1, which is chemically (3S)-N-{4-[(4-chlorophenyl)sulfanyl]phenyl}-3-hydroxypyrrolidine-1-carboxamide could function as a significant "seed" ligand for future design of potent AChE inhibitors and/or novel neuro drugs built upon the seed-scaffold.
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Affiliation(s)
- Shazi Shakil
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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21
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Khalid S, Zahid MA, Ali H, Kim YS, Khan S. Biaryl scaffold-focused virtual screening for anti-aggregatory and neuroprotective effects in Alzheimer's disease. BMC Neurosci 2018; 19:74. [PMID: 30424732 PMCID: PMC6234579 DOI: 10.1186/s12868-018-0472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 11/03/2018] [Indexed: 02/06/2023] Open
Abstract
Background Alzheimer’s disease (AD) is a primary cause of dementia in ageing population affecting more than 35 million people around the globe. It is a chronic neurodegenerative disease caused by defected folding and aggregation of amyloid beta (Aβ) protein. Aβ is formed by the cleavage of membrane embedded amyloid precursor protein (APP) by using enzyme ‘transmembrane aspartyl protease, β-secretase’. Inhibition of β-secretase is a viable strategy to prevent neurotoxicity in AD. Another strategy in the treatment of AD is inhibition of acetylcholinesterase. This inhibition reduces the degradation of acetylcholine and temporarily restores the cholinergic function of neurons and improves cognitive function. Monoamine oxidase and higher glutamate levels are also found to be linked with Aβ peptide related oxidative stress. Oxidative stress leads to reduced activity of glutamate synthase resulting in significantly higher level of glutamate in brain. The aim of this study is to perform in silico screening of a virtual library of biaryl scaffold containing compounds potentially used for the treatment of AD. Screening was done against the primary targets of AD therapeutics, acetylcholinesterase, β-secretase (BACE1), Monoamine oxidases (MAO) and N-Methyl-D-aspartate (NMDA) receptor. Compounds were screened for their inhibitory potential by employing molecular docking approach using AutoDock vina. Binding energy scores were embodied in the heatmap to display varies strengths of interactions of the ligands targeting AD. Results Several ligands showed notable interaction with at least two targets, but the strong interaction with all the targets is shown by very few ligands. The pharmacokinetics of the interacting ligands was also predicted. The interacting ligands have good drug-likeness and brain availability essential for drugs with intracranial targets. Conclusion These results suggest that biaryl scaffold may be pliable to drug development for neuroprotection in AD and that the synthesis of further analogues to optimize these properties should be considered. Electronic supplementary material The online version of this article (10.1186/s12868-018-0472-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sidra Khalid
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ammar Zahid
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.,Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hussain Ali
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yeong S Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Salman Khan
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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22
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Kim H, Han H. Computer-Aided Multi-Target Management of Emergent Alzheimer's Disease. Bioinformation 2018; 14:167-180. [PMID: 29983487 PMCID: PMC6016757 DOI: 10.6026/97320630014167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) represents an enormous global health burden in terms of human suffering and economic cost. AD management requires a shift from the prevailing paradigm targeting pathogenesis to design and develop effective drugs with adequate success in clinical trials. Therefore, it is of interest to report a review on amyloid beta (Aβ) effects and other multi-targets including cholinesterase, NFTs, tau protein and TNF associated with brain cell death to be neuro-protective from AD. It should be noted that these molecules have been generated either by target-based or phenotypic methods. Hence, the use of recent advancements in nanomedicine and other natural compounds screening tools as a feasible alternative for circumventing specific liabilities is realized. We review recent developments in the design and identification of neuro-degenerative compounds against AD generated using current advancements in computational multi-target modeling algorithms reflected by theragnosis (combination of diagnostic tests and therapy) concern.
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Affiliation(s)
- Hyunjo Kim
- Department of Medical Informatics, Ajou Medical University Hospital, Suwon, Kyeounggido province, South Korea
| | - Hyunwook Han
- Department of Informatics, School of Medicine, CHA University, Seongnam, South Korea
- Institute of Basic Medical Sciences, School of Medicine, CHA University, Seongnam, South Korea
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23
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Kumar A, Srivastava G, Negi AS, Sharma A. Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β. J Biomol Struct Dyn 2018; 37:275-290. [DOI: 10.1080/07391102.2018.1426043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Arvind S. Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
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24
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Kumar A, Sharma A. Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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25
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26
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Roy S, Gumulec J, Kumar A, Raudenska M, Baig MH, Polanska H, Balvan J, Gupta M, Babula P, Odstrčilík J, Choi I, Provaznik I, Masarik M. The effect of Benzothiazolone-2 on the expression of Metallothionein-3 in modulating Alzheimer's disease. Brain Behav 2017; 7:e00799. [PMID: 28948092 PMCID: PMC5607561 DOI: 10.1002/brb3.799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 06/14/2017] [Accepted: 07/02/2017] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Metallothioneins (MTs) are a class of ubiquitously occurring low-molecular-weight cysteine- and metal-rich proteins containing sulfur-based metal clusters. MT-3 exhibits neuro-inhibitory activity. The possibility to enhance the expression of MT-3 or protect it from degradation is an attractive therapeutic target, because low levels of MT-3 were found in brains of Alzheimer's disease (AD) patients. OBJECTIVES The primary objective of this study was to test an enhancement of MT-3 cellular concentration after MT-3 binding treatment, which could prevent MT-3 degradation. METHODS MTT assay, flow-cytometry, fluorescence microscopy, quantitative real-time polymerase chain reaction, and immunodetection of MT3 were used for analysis of effect of STOCK1N-26544, STOCK1N-26929, and STOCK1N-72593 on immortalized human microglia-SV40 cell line. RESULTS All three tested compounds enhanced concentration of MT-3 protein in cells and surprisingly also mRNA concentration. IC50 values of tested molecules exceeded about ten times the concentration that was needed for induction of MT-3 expression. The tested compound Benzothiazolone-2 enhanced apoptosis and necrosis, but it was not of severe effect. About 80% of cells were still viable. There was no serious ROS-generation and no severe decrease in mitochondria numbers or stress induced endoplasmic reticulum changes after test treatments. The selected compound showed stable hydrophobic and electrostatic interaction during MT-3 ligand interaction. CONCLUSION Benzothiazolone-2 compounds significantly enhanced MT-3 protein and mRNA levels. The compounds can be looked upon as one of the probable lead compounds for future drug designing experiments in the treatment of Alzheimer's disease.
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Affiliation(s)
- Sudeep Roy
- Department of Biomedical Engineering Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czech Republic
| | - Jaromir Gumulec
- Central European Institute of Technology Brno University of Technology Brno Czech Republic.,Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic.,Department of Pathological Physiology Faculty of Medicine, Masaryk University Brno Czech Republic
| | - Akhil Kumar
- Biotechnology Division CSIR-Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Martina Raudenska
- Central European Institute of Technology Brno University of Technology Brno Czech Republic.,Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic
| | | | - Hana Polanska
- Central European Institute of Technology Brno University of Technology Brno Czech Republic.,Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic.,Department of Pathological Physiology Faculty of Medicine, Masaryk University Brno Czech Republic
| | - Jan Balvan
- Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic.,Department of Pathological Physiology Faculty of Medicine, Masaryk University Brno Czech Republic
| | - Mansi Gupta
- Biotechnology Division CSIR-Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Petr Babula
- Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic
| | - Jan Odstrčilík
- Department of Biomedical Engineering Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czech Republic
| | - Inho Choi
- School of Biotechnology Yeungnam University Gyeongsan Korea
| | - Ivo Provaznik
- Department of Biomedical Engineering Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czech Republic.,Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic
| | - Michal Masarik
- Central European Institute of Technology Brno University of Technology Brno Czech Republic.,Department of Physiology Faculty of Medicine Masaryk University Brno Czech Republic.,Department of Pathological Physiology Faculty of Medicine, Masaryk University Brno Czech Republic
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27
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Novel ligand-based docking; molecular dynamic simulations; and absorption, distribution, metabolism, and excretion approach to analyzing potential acetylcholinesterase inhibitors for Alzheimer's disease. J Pharm Anal 2017; 8:413-420. [PMID: 30595949 PMCID: PMC6308024 DOI: 10.1016/j.jpha.2017.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/02/2022] Open
Abstract
Acetylcholinesterase (AChE) plays an important role in Alzheimer's disease (AD). The excessive activity of AChE causes various neuronal problems, particularly dementia and neuronal cell deaths. Generally, anti-AChE drugs induce some serious neuronal side effects in humans. Therefore, this study sought to identify alternative drug molecules from natural products with fewer side effects than those of conventional drugs for treating AD. To achieve this, we developed computational methods for predicting drug and target binding affinities using the Schrodinger suite. The target and ligand molecules were retrieved from established databases. The target enzyme has 539 amino acid residues in its sequence alignment. Ligand molecules of 20 bioactive molecules were obtained from different kinds of plants, after which we performed critical analyses such as molecular docking; molecular dynamic (MD) simulations; and absorption, distribution, metabolism, and excretion (ADME) analysis. In the docking studies, the natural compound rutin showed a superior docking score of −12.335 with a good binding energy value of −73.313 kcal/mol. Based on these findings, rutin and the target complex was used to perform MD simulations to analyze rutin stability at 30 ns. In conclusion, our study demonstrates that rutin is a superior drug candidate for AD. Therefore, we propose that this molecule is worth further investigation using in vitro studies.
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Nikolic K, Mavridis L, Djikic T, Vucicevic J, Agbaba D, Yelekci K, Mitchell JBO. Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies. Front Neurosci 2016; 10:265. [PMID: 27375423 PMCID: PMC4901078 DOI: 10.3389/fnins.2016.00265] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
HIGHLIGHTSMany CNS targets are being explored for multi-target drug design New databases and cheminformatic methods enable prediction of primary pharmaceutical target and off-targets of compounds QSAR, virtual screening and docking methods increase the potential of rational drug design
The diverse cerebral mechanisms implicated in Central Nervous System (CNS) diseases together with the heterogeneous and overlapping nature of phenotypes indicated that multitarget strategies may be appropriate for the improved treatment of complex brain diseases. Understanding how the neurotransmitter systems interact is also important in optimizing therapeutic strategies. Pharmacological intervention on one target will often influence another one, such as the well-established serotonin-dopamine interaction or the dopamine-glutamate interaction. It is now accepted that drug action can involve plural targets and that polypharmacological interaction with multiple targets, to address disease in more subtle and effective ways, is a key concept for development of novel drug candidates against complex CNS diseases. A multi-target therapeutic strategy for Alzheimer‘s disease resulted in the development of very effective Multi-Target Designed Ligands (MTDL) that act on both the cholinergic and monoaminergic systems, and also retard the progression of neurodegeneration by inhibiting amyloid aggregation. Many compounds already in databases have been investigated as ligands for multiple targets in drug-discovery programs. A probabilistic method, the Parzen-Rosenblatt Window approach, was used to build a “predictor” model using data collected from the ChEMBL database. The model can be used to predict both the primary pharmaceutical target and off-targets of a compound based on its structure. Several multi-target ligands were selected for further study, as compounds with possible additional beneficial pharmacological activities. Based on all these findings, it is concluded that multipotent ligands targeting AChE/MAO-A/MAO-B and also D1-R/D2-R/5-HT2A-R/H3-R are promising novel drug candidates with improved efficacy and beneficial neuroleptic and procognitive activities in treatment of Alzheimer's and related neurodegenerative diseases. Structural information for drug targets permits docking and virtual screening and exploration of the molecular determinants of binding, hence facilitating the design of multi-targeted drugs. The crystal structures and models of enzymes of the monoaminergic and cholinergic systems have been used to investigate the structural origins of target selectivity and to identify molecular determinants, in order to design MTDLs.
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Affiliation(s)
- Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Lazaros Mavridis
- School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Teodora Djikic
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University Istanbul, Turkey
| | - Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Danica Agbaba
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Kemal Yelekci
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University Istanbul, Turkey
| | - John B O Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews St Andrews, UK
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Wang J, Shu M, Wang Y, Hu Y, Wang Y, Luo Y, Lin Z. Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis. MOLECULAR BIOSYSTEMS 2016; 12:3396-3406. [DOI: 10.1039/c6mb00577b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Employing the combined strategy to identify novel CCR5 inhibitors and provide a basis for rational drug design.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yong Hu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Yanfeng Luo
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
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30
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Affiliation(s)
- Sun Kim
- Seoul National University, Seoul, South Korea
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