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Rehman HM, Sajjad M, Ali MA, Gul R, Irfan M, Naveed M, Bhinder MA, Ghani MU, Hussain N, Said ASA, Al Haddad AHI, Saleem M. Identification of NS2B-NS3 Protease Inhibitors for Therapeutic Application in ZIKV Infection: A Pharmacophore-Based High-Throughput Virtual Screening and MD Simulations Approaches. Vaccines (Basel) 2023; 11:vaccines11010131. [PMID: 36679976 PMCID: PMC9862652 DOI: 10.3390/vaccines11010131] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) pandemic and its implication in congenital malformations and severe neurological disorders had created serious threats to global health. ZIKV is a mosquito-borne flavivirus which spread rapidly and infect a large number of people in a shorter time-span. Due to the lack of effective therapeutics, this had become paramount urgency to discover effective drug molecules to encounter the viral infection. Various anti-ZIKV drug discovery efforts during the past several years had been unsuccessful to develop an effective cure. The NS2B-NS3 protein was reported as an attractive therapeutic target for inhibiting viral proliferation, due to its central role in viral replication and maturation of non-structural viral proteins. Therefore, the current in silico drug exploration aimed to identify the novel inhibitors of Zika NS2B-NS3 protease by implementing an e-pharmacophore-based high-throughput virtual screening. A 3D e-pharmacophore model was generated based on the five-featured (ADPRR) pharmacophore hypothesis. Subsequently, the predicted model is further subjected to the high-throughput virtual screening to reveal top hit molecules from the various small molecule databases. Initial hits were examined in terms of binding free energies and ADME properties to identify the candidate hit exhibiting a favourable pharmacokinetic profile. Eventually, molecular dynamic (MD) simulations studies were conducted to evaluate the binding stability of the hit molecule inside the receptor cavity. The findings of the in silico analysis manifested affirmative evidence for three hit molecules with -64.28, -55.15 and -50.16 kcal/mol binding free energies, as potent inhibitors of Zika NS2B-NS3 protease. Hence, these molecules holds the promising potential to serve as a prospective candidates to design effective drugs against ZIKV and related viral infections.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Muhammad Akhtar Ali
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan
| | - Muhammad Irfan
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore 54600, Punjab, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab Lahore, Lahore 54590, Punjab, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Usman Ghani
- Center for Applied Molecular Biology, University of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Amira S. A. Said
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- Department of Clinical Pharmacy, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni Suef University, Beni Suef 62521, Egypt
| | - Amal H. I. Al Haddad
- Chief Operations Office, Sheikh Shakhbout Medical City (SSMC) in Partnership with Mayo Clinic, Abu Dhabi 11001, United Arab Emirates
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- School of Medical Lab Technology, Minhaj University Lahore, Lahore 54770, Punjab, Pakistan
- Correspondence:
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Zhong ZJ, Hu XT, Cheng LP, Zhang XY, Zhang Q, Zhang J. Discovery of novel thiophene derivatives as potent neuraminidase inhibitors. Eur J Med Chem 2021; 225:113762. [PMID: 34411893 DOI: 10.1016/j.ejmech.2021.113762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 10/20/2022]
Abstract
Neuraminidase (NA) is an important target for the treatment of influenza. In this study, a new lead NA inhibitor, 4 (ZINC01121127), was discovered by pharmacophore-based virtual screening and molecular dynamic (MD) simulation. Some novel NA inhibitors containing thiophene ring were synthesized by optimizing the skeleton of the lead compound 4. Compound 4b had the most potent inhibitory activity against NA (IC50 = 0.03 μM), which was better than the positive control oseltamivir carboxylate (IC50 = 0.06 μM). 4b (EC50 = 1.59 μM) also exhibits excellent antiviral activity against A/chicken/Hubei/327/2004 (H5N1-DW), which is superior to the reference drug OSC (EC50 = 5.97 μM). Molecular docking study shows that the thiophene moiety plays an essential role in compound 4b, which can bind well to the active site of NA. The good activity of 4b may be also ascribed to the extending of quinoline ring into the 150-cavity. The results of this study may provide an insightful help for the development of new NA inhibitors.
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Affiliation(s)
- Zhi Jian Zhong
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Xiao Tong Hu
- Unit of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li Ping Cheng
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, China.
| | - Xing Yong Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Qiang Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Ju Zhang
- Wuhan Yangene Biological Technology Co, LTD, Yuechuang Center of Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Tolmie M, Bester MJ, Apostolides Z. Inhibition of α-glucosidase and α-amylase by herbal compounds for the treatment of type 2 diabetes: A validation of in silico reverse docking with in vitro enzyme assays. J Diabetes 2021; 13:779-791. [PMID: 33550683 DOI: 10.1111/1753-0407.13163] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/25/2021] [Accepted: 02/03/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND α-Amylase and α-glucosidase are important therapeutic targets for the management of type 2 diabetes mellitus. The inhibition of these enzymes decreases postprandial hyperglycemia. In the present study, compounds found in commercially available herbs and spices were tested for their ability to inhibit α-amylase and α-glucosidase. These compounds were acetyleugenol, apigenin, cinnamic acid, eriodictyol, myrcene, piperine, and rosmarinic acid. METHODS The enzyme inhibitory nature of the compounds was evaluated using in silico docking analysis with Maestro software and was further confirmed by in vitro α-amylase and α-glucosidase biochemical assays. RESULTS The relationships between the in silico and in vitro results were well correlated; a more negative docking score was associated with a higher in vitro inhibitory activity. There was no significant (P > .05) difference between the inhibition constant (Ki ) value of acarbose, a widely prescribed α-glucosidase and α-amylase inhibitor, and those of apigenin, eriodictyol, and piperine. For α-amylase, there was no significant (P > .05) difference between the Ki value of acarbose and those of apigenin, cinnamic acid, and rosmarinic acid. The effect of the herbal compounds on cell viability was assessed with the sulforhodamine B (SRB) assay in C2C12 and HepG2 cells. Acetyleugenol, cinnamic acid, myrcene, piperine, and rosmarinic acid had similar (P > .05) IC50 values to acarbose. CONCLUSIONS Several of the herbal compounds studied could regulate postprandial hyperglycemia. Using herbal plants has several advantages including low cost, natural origin, and easy cultivation. These compounds can easily be consumed as teas or as herbs and spices to flavor food.
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Affiliation(s)
- Morné Tolmie
- Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Megan Jean Bester
- Department of Anatomy, University of Pretoria, Pretoria, South Africa
| | - Zeno Apostolides
- Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, South Africa
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4
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Duan C, Liu W, Chen L, Pan J, Liu Y, Lin K, Zhou W. Synthesis and 1H NMR data assignment of 3-acetamido-4-amino-3,4-dihydro-2H-pyran-6-carboxylates and their acetyl-migrated isomers. SYNTHETIC COMMUN 2021. [DOI: 10.1080/00397911.2021.1966038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Chuanqi Duan
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Weiyuan Liu
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Liang Chen
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Jing Pan
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Yubin Liu
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Kuaile Lin
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
| | - Weicheng Zhou
- State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, P. R. of China
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Xing S, Chen Y, Xiong B, Lu W, Li Q, Wang Y, Jiao M, Feng F, Chen Y, Liu W, Sun H. Synthesis and bio-evaluation of a novel selective butyrylcholinesterase inhibitor discovered through structure-based virtual screening. Int J Biol Macromol 2020; 166:1352-1364. [PMID: 33161083 DOI: 10.1016/j.ijbiomac.2020.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/14/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
In recent years, butyrylcholinesterase (BChE) has gradually gained worldwide interests as a novel target for treating Alzheimer's disease (AD). Here, two pharmacophore models were generated using Schrödinger suite and used to virtually screen ChemDiv database, from which three hits were obtained. Among them, 2513-4169 displayed the highest inhibitory activity and selectivity against BChE (eeAChE IC50 > 10 μM, eqBChE IC50 = 3.73 ± 1.90 μM). Molecular dynamic (MD) simulation validated the binding pattern of 2513-4169 in BChE, and it could form a various of receptor-ligand interactions with adjacent residues. In vitro cytotoxicity assay proved the safety of 2513-4169 on diverse neural cell lines. Moreover, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay performed on SH-SY5Y cells proved the neuroprotective effect of 2513-4169 against toxic Aβ1-42. In vivo behavioral study further confirmed the great efficacy of 2513-4169 on reversing Aβ1-42-induced cognitive impairment of mice and clearing the toxic Aβ1-42 in brains. Moreover, 2513-4169 was proved to be able to cross blood-brain barrier (BBB) through a parallel artificial membrane permeation assay of BBB (PAMPA-BBB). Taken together, 2513-4169 is a promising lead compound for future optimization to discover anti-AD treating agents.
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Affiliation(s)
- Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Ying Chen
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Baichen Xiong
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Weixuan Lu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qi Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yuanyuan Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Mengxia Jiao
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China; Jiangsu Food and Pharmaceutical Science College, No.4 Meicheng Road, Huai'an 223003, People's Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Wenyuan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China.
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China.
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6
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Xu Z, Yang L, Zhang X, Zhang Q, Yang Z, Liu Y, Wei S, Liu W. Discovery of Potential Flavonoid Inhibitors Against COVID-19 3CL Proteinase Based on Virtual Screening Strategy. Front Mol Biosci 2020; 7:556481. [PMID: 33134310 PMCID: PMC7561382 DOI: 10.3389/fmolb.2020.556481] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
The outbreak of 2019 novel coronavirus (COVID-19) has caused serious threat to public health. Discovery of new anti-COVID-19 drugs is urgently needed. Fortunately, the crystal structure of COVID-19 3CL proteinase was recently resolved. The proteinase has been identified as a promising target for drug discovery in this crisis. Here, a dataset including 2030 natural compounds was screened and refined based on the machine learning and molecular docking. The performance of six machine learning (ML) methods of predicting active coronavirus inhibitors had achieved satisfactory accuracy, especially, the AUC (Area Under ROC Curve) scores with fivefold cross-validation of Logistic Regression (LR) reached up to 0.976. Comprehensive ML prediction and molecular docking results accounted for the compound Rutin, which was approved by NMPA (National Medical Products Administration), exhibited the best AUC and the most promising binding affinity compared to other compounds. Therefore, Rutin might be a promising agent in anti-COVID-19 drugs development.
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Affiliation(s)
- Zhongren Xu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | | | - Xinghao Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiling Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhibin Yang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanhao Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuang Wei
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wukun Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine and Holistic Integrative Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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7
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James N, Shanthi V, Ramanathan K. Density Functional Theory and Molecular Simulation Studies for Prioritizing Anaplastic Lymphoma Kinase Inhibitors. Appl Biochem Biotechnol 2019; 190:1127-1146. [PMID: 31712989 DOI: 10.1007/s12010-019-03156-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022]
Abstract
Targeting anaplastic lymphoma kinase (ALK) is one of the important treatment strategies for the treatment of non-small cell lung cancer (NSCLC). In the present perspective, multidimensional approaches were used for the identification of ALK inhibitors. Initially, an e-pharmacophore model was generated using the PHASE algorithm and was used as a 3D query to screen 468,200 molecules of ASINEX database. Prior to the screening process, the model was evaluated for its significance and the ability to differentiate actives from inactives, using enrichment analysis. Subsequently, the hierarchical docking protocol and binding free energy calculations were instigated using GLIDE algorithm and Prime module, respectively. Further, the pharmacokinetic/pharmacodynamics (PK/PD) properties and toxicities of the hit compounds were envisaged respectively using QikProp program, Osiris explorer, and Protox-II algorithm. These approaches retrieved two hits namely BAS 00137817 and BAS 00680055 with acceptable absorption, distribution, metabolism, excretion and toxicity (ADMET) properties and higher affinity towards ALK protein. Additionally, density functional theory calculations and molecular dynamics simulations were performed to validate the inhibitory activity of the lead compounds. It is noteworthy to mention that all the hits constitute of particular scaffolds which play a major role in the downregulation of some ALK-positive lung cancer pathways. We speculate that the outcomes of this research are of substantial prominence in the rational designing of novel and efficacious ALK inhibitors.
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Affiliation(s)
- Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - K Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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8
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Rohini K, Ramanathan K, Shanthi V. Multi-Dimensional Screening Strategy for Drug Repurposing with Statistical Framework—A New Road to Influenza Drug discovery. Cell Biochem Biophys 2019; 77:319-333. [DOI: 10.1007/s12013-019-00887-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
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Rohini K, Roy R, Ramanathan K, Shanthi V. E-pharmacophore hypothesis strategy to discover potent inhibitor for influenza treatment. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The surface protein of Influenza virus, Neuraminidase (NA), is believed to play a critical role in the release of new viral particle and thus spreads infection. It has been recognized as a valid drug target for anti-influenza therapy. Despite the number of available approved drugs for the influenza infection treatment, the emergence of resistant variants with novel mutations are the foremost challenges for the currently used NA inhibitors. Thus, the current investigation was carried out to ascertain potent inhibitors using computational strategies such as e-pharmacophore based virtual screening and docking approach. A three-dimensional e-pharmacophore hypothesis was generated based on the chemical features of complexes of the drugs and NA protein using PHASE module of Schrödinger suite. The generated hypothesis consisted of one hydrogen bond acceptor (A), two hydrogen bond donors (D), one negatively charged group (N) and one aromatic ring (R), ADDNR. The hypothesis was further evaluated for its integrity using enrichment analysis and used to filter out molecules with similar pharmacophoric features from approved, investigational and experimental subsets of DrugBank and ZINC database. In addition, ligand filtration was performed to curb down the molecules to an efficient collection of hit molecules by using Lipinski “rule of five and ADME analysis by using Qikprop module. Overall, the results from our analysis suggest that compound lisinopril and formoterol could serve as potent antiviral compounds for the treatment of influenza A virus infection. It is worth mentioning that the results correlate well with literature evidences.
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Affiliation(s)
- K. Rohini
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Roosha Roy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - K. Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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10
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James N, Shanthi V, Ramanathan K. Discovery of novel anaplastic lymphoma kinase inhibitors: Structure and energy-based pharmacophore strategy. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), which were then subjected to molecular docking and ADME prediction. These approaches resulted in the identification of five hits, namely, nebivolol, HDY, D42, 796, and LZE having higher Glide docking scores and promising ADME properties with augmented CNS involvement. Moreover, molecular dynamics simulations were performed to validate the inhibitory activity of the hit compounds, and density functional theory calculations were carried out to scrutinize the chemical reactivity of the hits. Subsequent interaction and scaffold analysis identified prominent interactions of the hits with ALK kinase domain and scaffolds with anti-tumor activity against lung cancer cell lines. We strongly believe that the study provides an outlook for the sighting of novel and potent ALK inhibitors in the near future.
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Affiliation(s)
- Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - K. Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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11
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Bolelli K, Ertan-Bolelli T. Pharmacophore-Based Virtual Screening of Novel GSTP1-1 Inhibitors. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2018. [DOI: 10.18596/jotcsa.466458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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12
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Rohini K, Agarwal P, Preethi B, Shanthi V, Ramanathan K. Exploring the Lead Compounds for Zika Virus NS2B-NS3 Protein: an e-Pharmacophore-Based Approach. Appl Biochem Biotechnol 2018; 187:194-210. [PMID: 29911269 DOI: 10.1007/s12010-018-2814-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/05/2018] [Indexed: 12/19/2022]
Abstract
The rapid spread of the Zika virus and its association with the abnormal brain development constitute a global health emergency. With a continuing spread of the mosquito vector, the exposure is expected to accelerate in the coming years. Despite number of efforts, there is still no proper vaccine or medicine to combat this virus. Of note, the NS2B-NS3 protein is proven to be the potential target for the Zika virus therapeutics. Hence, e-pharmacophore-based drug design strategy was employed to identify potent inhibitors of NS2B-NS3 protein from ASINEX database consisting of 467,802 molecules. A 3D e-pharmacophore model was generated using PHASE module of Schrödinger Suite. The generated model consists of one hydrogen bond acceptor (A), two hydrogen bond donors (D), and two aromatic rings (R), ADDRR. The model was further evaluated for its ability to screen actives using enrichment analysis. Subsequently, high-throughput virtual screening protocol was employed, and the resultant hit molecules were also examined for its binding free energies and ADME properties using Prime MM-GBSA and Qikprop module of Schrodinger packages, respectively. Finally, the screened hit molecule was subjected to molecular dynamics simulation to examine its stability. Overall, the results from our analysis suggest that compound BAS 19192837 could be a potent inhibitor for the NS2B-NS3 protein of the Zika virus. It is also noteworthy to mention that our results are in good agreement with literature evidences. We hope that this result is of immense importance in designing potential drug molecules to combat the spread of Zika virus in the near future.
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Affiliation(s)
- K Rohini
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - Pratika Agarwal
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - B Preethi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - K Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India.
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13
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Kozhikkadan Davis C, Nasla K, Anjana AK, Rajanikant GK. Taxifolin as dual inhibitor of Mtb DNA gyrase and isoleucyl-tRNA synthetase: in silico molecular docking, dynamics simulation and in vitro assays. In Silico Pharmacol 2018; 6:8. [PMID: 30607321 DOI: 10.1007/s40203-018-0045-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 04/05/2018] [Indexed: 12/25/2022] Open
Abstract
DNA gyrase and aminoacyl-tRNA synthetases are two essential bacterial enzymes involved in DNA replication, transcription and translation. Flavonoids are plant secondary metabolites with variable phenolic structures. In this study, eight flavonoids structurally similar to quercetin were selected and their ADMET properties were evaluated. Molecular docking and free energy calculations were carried out to examine the binding of these flavonoids to the ATP-binding site and editing domain of DNA gyrase and Isoleucyl-tRNA synthetase, respectively. Taxifolin was found out to be the top lead molecule in both the docking studies with a good number of interactions with the active site amino acids. Further, binding of taxifolin to the proteins was extensively studied using 50 ns molecular dynamics simulation. In vitro anti-tuberculosis activity of taxifolin was evaluated and compared with the standard drugs. Minimal inhibition concentration of taxifolin was found to be ≤ 12.5 μg/ml.
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Affiliation(s)
| | - K Nasla
- Department of Pharmacognosy and Phytochemistry, Jamia Salafiya Pharmacy College, Malappuram, 673637 India
| | - A K Anjana
- Department of Pharmacognosy and Phytochemistry, Jamia Salafiya Pharmacy College, Malappuram, 673637 India
| | - G K Rajanikant
- 1School of Biotechnology, National Institute of Technology Calicut, Calicut, 673601 India
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