1
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Wang X, Ye CH, Li EM, Xu LY, Lin WQ, Chen GH. Discovery of octahydropyrrolo [3,2-b] pyridin derivative as a highly selective Type I inhibitor of FGFR3 over VEGFR2 by high-throughput virtual screening. J Cell Biochem 2023; 124:221-238. [PMID: 36502529 DOI: 10.1002/jcb.30357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/17/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Although the aberrant activity of fibroblast growth factor receptor 3 (FGFR3) is implicated in various cancers, the reported kinase inhibitors of FGFR3 tend to cause side effects resulting from the inhibitory activity on vascular endothelial growth factor receptor 2 (VEGFR2). Therefore, it is necessary to find a novel high-selective inhibitor of FGFR3 over VEGFR2 from the small-molecule compound database. In this study, integrated virtual screening protocols were established to screen for selective inhibitors of FGFR3 over VEGFR2 in Drugbank and Asinex databases by combining three-dimensional pharmacophore model, molecular docking, molecular dynamics (MD) simulation, and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations. Finally, it is found that Asinex-5082, as an octahydropyrrolo[3,2-b] pyridin derivative, has larger binding free energy with FGFR3 (-39.3 kcal/mol) than reference drug Erdafitinib (-29.9 kcal/mol), while cannot bind with VEGFR2, resulting in considerable inhibitory selectivity. This is because Asinex-5082, unlike Erdafitinib, has not m-dimethoxybenzene with large steric hindrance, thus can enter the larger ATP-binding pocket of FGFR3 with DFG-in conformation to form hydrophobic interaction with residues Met529, Ile539, and Tyr557 as well as hydrogen bond with Ala558. On the other hand, due to the fact that the benzodioxane and N-heterocyclic rings are connected by carbonyl (C=O), Asinex-5082 cannot rotate freely so as to enter the smaller ATP binding pocket of VEGFR2 on the DFG-out conformation. The lead molecule Asinex-5082 may facilitate the rational design and development of novel selective inhibitors of FGFR3 over VEGFR2 as anticancer drugs.
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Affiliation(s)
- Xin Wang
- Department of Chemistry, Shantou University, Shantou, China
| | - Cheng-Hao Ye
- Department of Chemistry, Shantou University, Shantou, China
| | - En-Min Li
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
| | - Li-Yan Xu
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
| | - Wang-Qiang Lin
- Department of Chemistry, Shantou University, Shantou, China
| | - Guang-Hui Chen
- Department of Chemistry, Shantou University, Shantou, China
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2
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Identification of missense SNP-mediated mutations in the regulatory sites of aldose reductase (ALR2) responsible for treatment failure in diabetic complications. J Mol Model 2022; 28:260. [PMID: 35984530 DOI: 10.1007/s00894-022-05256-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 07/31/2022] [Indexed: 10/15/2022]
Abstract
Scientific pieces of evidence indicate that the polymorphism in the ALR2 regulatory gene favors the susceptibility to diabetic complications (DCs). Previous studies have uncovered several single nucleotide polymorphisms (SNPs) in the ALR2 regulatory sites that negatively modulate the activity of this enzyme and eventually increase the risks of DCs. In view of this, the current study aimed at investigating whether the mutation as a resultant of missense SNPs in the regulatory site of ALR2 enzyme can also hamper the interactions of ALR2 inhibitors with the key amino acid residues in the ALR2 binding site. Around 202 SNPs in the ALR2 gene were reported in the dbSNP database. Out of these, eighteen SNPs that are responsible for point mutations in the regulatory sites of ALR2 enzyme were identified and considered for the study. Identified SNPs were then categorized as stabilizing or destabilizing using various in silico tools and webservers. The resulting mutational constructs of ALR2 were further probed for their influence on the binding affinities and binding modes with well-known ALR2 inhibitors using structure-based analyses. This study identified three destabilizing SNPs, i.e., rs779176563 (C298S), rs1392886142 (G16A), and rs1407261115 (A245T), that lead to the compromised response to most of the ALR2 inhibitors which are in clinical trials. On the other hand, treatment with these ALR2 inhibitors may benefit the population which carries missense SNPs rs748119899, rs1402962430, and rs1467939858 that code for W219S, Q183V, and S214A, respectively. Overall findings of the study suggest that one SNP in the inhibitor site and two SNPs in the co-factor site of ALR2 may be responsible for the low efficacy and unsuccessful journey of ALR2 inhibitors in the clinical trials.
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3
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Saranyadevi S. Multifaceted targeting strategies in cancer against the human notch 3 protein: a computational study. In Silico Pharmacol 2021; 9:53. [PMID: 34631360 DOI: 10.1007/s40203-021-00112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022] Open
Abstract
Notch receptors play a significant role in the development and the regulation of cell-fate in several multicellular organisms. For normal differentiation, genomes are essential as their regular roles and play a role in cancer is dysregulated. Notch 3 has been shown to play a major role in lung cancer function and therefore, inhibition of notch 3 protein activation represents a clear plan for cancer treatment. This study accomplished a combined structure- and ligand-based pharmacophore hypothesis to explore novel notch 3 inhibitors. The analysis identified common lead molecule ZINC000013449462 that showed better XP GScore and binding energy score than the reference inhibitor DAPT. The identified lead compound that passed all the druggable characteristics exhibited stable binding. Furthermore, the lead molecule can also form hydrogen and salt bridge interactions with binding site residues Asp1621 and Arg1465 residues, respectively of the active pockets of notch 3 protein. In essence, the inhibitory activity of the hit was validated across 109 NSCLC cell lines by employing a deep neural network algorithm. Our study proposes that ZINC000013449462 would be a possible prototype molecule towards the notch 3 target and further examined by clinical studies to combat NSCLC.
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Affiliation(s)
- S Saranyadevi
- Department of Nanotechnology, Nanodot Research Private Limited, Nagercoil, Kanyakumari, 629001 India
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4
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Jadoon MH, Rehman Z, Khan A, Rizwan M, Khan S, Mehmood A, Munir A. In silico T-cell and B-cell Epitope Based Vaccine Design Against Alphavirus Strain of Chikungunya. Infect Disord Drug Targets 2020; 20:523-530. [PMID: 31109281 DOI: 10.2174/1871526519666190521100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Chikungunya an arbovirus, is transmitted to humans by the bite of Aedes mosquito. The virus occurrences have been reported in Southeast Asian countries including Pakistan. Its symptoms include typical febrile illness and arthralgic syndrome. The virus has not decisively proved to be life-threatening. METHODS The attempt was to design T-cell and B-cell epitope-based vaccine for Chikungunya. The proteome of chikungunya was retrieved, antigenic proteins were identified and T-cell epitopes and B-cell epitopes were predicted. Interacting HLA alleles were also identified. The final analysis was done to confirm that predicted T-cell epitopes and B-cell epitopes can be used as a vaccine. RESULTS About 32 T-cell epitopes and a 10mer B-cell epitope were identified. Both T-cell and Bcell epitopes demonstrated strong interactions with HLA alleles. The predicted T-cell and B-cell epitopes were docked with respective HLA alleles. The docking analysis showed that the predicted respective epitopes best fit into the binding pockets of the alleles. CONCLUSION On the basis of this computational analysis, it is suggested that these predicted epitopes can be used as a remedy against Alphavirus strain of chikungunya. Further laboratory experiments can be conducted to determine the efficacy and stability of this work.
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Affiliation(s)
- Maharij Haroon Jadoon
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Zainab Rehman
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Areeba Khan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Muhammad Rizwan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Sajid Khan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Azhar Mehmood
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Anum Munir
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
- Department of Bioinformatics, Capital University of Science and Technology, Islamabad, Pakistan
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5
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Sharma D, Kumar S, Narasimhan B, Ramasamy K, Lim SM, Shah SAA, Mani V. 4-(4-Bromophenyl)-thiazol-2-amine derivatives: synthesis, biological activity and molecular docking study with ADME profile. BMC Chem 2019; 13:60. [PMID: 31384808 PMCID: PMC6661755 DOI: 10.1186/s13065-019-0575-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
In order to overcome the challenges of microbial resistance as well as to improve the effectiveness and selectivity of chemotherapeutic agents against cancer, a novel series of 4-(4-bromophenyl)-thiazol-2-amine derivatives was synthesized and its molecular structures were confirmed by physicochemical and spectral characteristics. The synthesized compounds were further evaluated for their in vitro antimicrobial activity using turbidimetric method and anticancer activity against oestrogen receptor positive human breast adenocarcinoma cancer cell line (MCF7) by Sulforhodamine B (SRB) assay. The antimicrobial activity results revealed that compound p2, p3, p4 and p6 exhibited promising antimicrobial activity that are comparable to standard norfloxacin (antibacterial) and fluconazole (antifungal). Anticancer screening results demonstrated that compound p2 was found to be the most active one against cancer cell line when compared to the rest of the compounds and comparable to the standard drug (5-fluorouracil). The molecular docking study demonstrated that compounds, p2, p3, p4 and p6 displayed good docking score within binding pocket of the selected PDB ID (1JIJ, 4WMZ and 3ERT) and showed promising ADME properties.
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Affiliation(s)
- Deepika Sharma
- 1Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001 India
| | - Sanjiv Kumar
- 1Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001 India
| | | | - Kalavathy Ramasamy
- 2Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan Malaysia.,3Collaborative Drug Discovery Research (CDDR) Group, Pharmaceutical Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan Malaysia
| | - Siong Meng Lim
- 2Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan Malaysia.,3Collaborative Drug Discovery Research (CDDR) Group, Pharmaceutical Life Sciences Community of Research, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor Darul Ehsan Malaysia
| | - Syed Adnan Ali Shah
- 2Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan Malaysia.,4Atta-ur-Rahman Institute for Natural Products Discovery (AuRIns), Universiti Teknologi MARA, 42300 Bandar Puncak Alam, Selangor Darul Ehsan Malaysia
| | - Vasudevan Mani
- 5Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraidah, 51452 Kingdom of Saudi Arabia
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Zakerali T, Shahbazi S. Rational Druggability Investigation Toward Selection of Lead Molecules: Impact of the Commonly Used Spices on Inflammatory Diseases. Assay Drug Dev Technol 2018; 16:397-407. [DOI: 10.1089/adt.2018.853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Tara Zakerali
- Department of Biotechnology, Tehran University, Tehran, Iran
| | - Sajad Shahbazi
- Department of Biotechnology, Panjab University, Chandigarh, India
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Yong T, Chen S, Xie Y, Shuai O, Li X, Chen D, Su J, Jiao C, Liang Y. Hypouricemic Effects of Extracts From Agrocybe aegerita on Hyperuricemia Mice and Virtual Prediction of Bioactives by Molecular Docking. Front Pharmacol 2018; 9:498. [PMID: 29867500 PMCID: PMC5962791 DOI: 10.3389/fphar.2018.00498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
Agrocybe aegerita has long been utilized for promoting diuresis in traditional Chinese medicine (TCM) with a close correlation to hypouricemia. Ethanol (AAE) and water (AAW) extracts of the compound led to a remarkable decrease in serum uric acid levels (SUA) in hyperuricemia mice, approaching that of the normal control. Both AAE and AAW exhibited suppression effects on hepatic xanthine oxidase (XOD) activities and elevation effects on renal OAT1 (organic anion transporter 1). However, only little negative impact was observed on the inner organ functions. The molecular docking was used to screen our in-home compound database for A. aegerita, and four compounds including 2-formyl-3,5-dihydroxybenzyl acetate, 2,4-dihydroxy-6-methylbenzaldehyde, 2-(6-hydroxy-1H-indol-3-yl)acetamide, and 6-hydroxy-1H-indole-3-carbaldehyde (HHC) were identified as potential active compounds. Their inhibitory mechanism on XOD might be attributed to their localization in the tunnel for the entrance of substrates to XOD active site, preventing the entrance of the substrates. To confirm the activity of the screened compounds experimentally, HHC was selected due to its high ranking and availability. The assaying result suggested the significant inhibitory activity of HHC on XOD. Also, these compounds were predicted to carry good ADME (absorption, distribution, metabolism, and excretion) properties, thereby necessitating further investigation. The current results provided an insight into the hypouricemic effects of macrofungi and their bioactives, which might provide the significant theoretical foundation for identifying and designing novel hypouricemia compounds.
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Affiliation(s)
- Tianqiao Yong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Shaodan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Yizhen Xie
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Ou Shuai
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Xiangmin Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Diling Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Jiyan Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Chunwei Jiao
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Yalei Liang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application and Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
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8
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Verma K, Kannan K, V S, R S, V K, K R. Exploring β-Tubulin Inhibitors from Plant Origin using Computational Approach. PHYTOCHEMICAL ANALYSIS : PCA 2017; 28:230-241. [PMID: 28008675 DOI: 10.1002/pca.2665] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 05/28/2023]
Abstract
INTRODUCTION β-Tubulin is an important target for the binding of anti-cancer drugs, in particular, paclitaxel (taxol), vinblastine and epothilone. However, mutations in β-tubulin structure give resistance to chemotherapeutic agents. Notably, mutations at R306C, F270 V, L217R, L228F, A185T and A248V positions in β-tubulin give high resistance for paclitaxel binding. OBJECTIVE To discover novel inhibitors of β-tubulin from natural sources, particularly alkaloids, using a virtual screening approach. METHODOLOGY A virtual screening approach was employed to find potent lead molecules from the Naturally-occurring Plant-based Anti-cancer Compound-activity Target (NPACT) database. Alkaloids have great potential to be anti-cancer agents. Therefore, we have screened all alkaloids from a total of 1574 molecules from the NPACT database for our study. Initially, Molinspiration and DataWarrior programs were utilised to calculate pharmacokinetics and toxicity risks of the alkaloids, respectively. Subsequently, AutoDock algorithm was employed to understand the binding efficiency of alkaloids against β-tubulin. The binding affinity of the docked complex was confirmed by means of an intermolecular interaction study. Moreover, oral toxicity was predicted by using ProTox program. Further, metabolising capacity of drugs was studied by using SmartCYP software. Additionally, scaffold analysis was done with the help of scaffold trees and dendrograms, providing knowledge about the building blocks for parent-compound synthesis. RESULTS Overall, the results of our computational analysis indicate that isostrychnine, obtained from Strychnosnux-vomica, satisfies pharmacokinetic and bioavailability properties, binds efficiently with β-tubulin. Thus, it could be a promising lead for the treatment of paclitaxel resistant cancer types. CONCLUSION This is the first observation of inhibitory activity of isostrychnine against β-tubulin and warrants further experimental investigation. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kanika Verma
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Kaavya Kannan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Shanthi V
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Sethumadhavan R
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Karthick V
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Ramanathan K
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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9
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Shahbazi S, Sahrawat TR, Ray M, Dash S, Kar D, Singh S. Drug Targets for Cardiovascular-Safe Anti-Inflammatory: In Silico Rational Drug Studies. PLoS One 2016; 11:e0156156. [PMID: 27258084 PMCID: PMC4892653 DOI: 10.1371/journal.pone.0156156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 05/10/2016] [Indexed: 02/06/2023] Open
Abstract
Cyclooxygenase-2 (COX-2) plays an important role in memory consolidation and synaptic activity, the most fundamental functions of the brain. It converts arachidonic acid to prostaglandin endoperoxide H2. In contrast, if over-expressed, it causes inflammation in response to cytokine, pro-inflammatory molecule, and growth factor. Anti-inflammatory agents, by allosteric or competitive inhibition of COX-2, alleviate the symptoms of inflammation. Coxib family drugs, particularly celecoxib, are the most famous anti-inflammatory agents available in the market showing significant inhibitory effect on COX-2 activity. Due to high cardiovascular risk of this drug group, recent researches are focused on the investigation of new safer drugs for anti-inflammatory diseases. Natural compounds, particularly, phytochemicals are found to be good candidates for drug designing and discovery. In the present study, we performed in silico studies to quantitatively scrutinize the molecular interaction of curcumin and its structural analogs with COX-2, COX-1, FXa and integrin αIIbβIII to investigate their therapeutic potential as a cardiovascular-safe anti-inflammatory medicine (CVSAIM). The results of both ADMET and docking study indicated that out of all the 39 compounds studied, caffeic acid had remarkable interaction with proteins involved in inflammatory response. It was also found to inhibit the proteins that are involved in thrombosis, thereby, having the potential to be developed as therapeutic agent.
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Affiliation(s)
- Sajad Shahbazi
- Department of Biotechnology, Punjab University, Chandigarh, India
| | - Tammanna R Sahrawat
- Centre for System Biology and Bioinformatics, Punjab University, Chandigarh, India
| | - Monalisa Ray
- Centre of Biotechnology, Siksha O Anusandhan University, Khandagiri, Bhubaneswar, Odisha, India
| | - Swagatika Dash
- Centre of Biotechnology, Siksha O Anusandhan University, Khandagiri, Bhubaneswar, Odisha, India
| | - Dattatreya Kar
- Centre of Biotechnology, Siksha O Anusandhan University, Khandagiri, Bhubaneswar, Odisha, India
| | - Shikha Singh
- Centre of Biotechnology, Siksha O Anusandhan University, Khandagiri, Bhubaneswar, Odisha, India
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10
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Wang J, Shu M, Wen X, Wang Y, Wang Y, Hu Y, Lin Z. Discovery of vascular endothelial growth factor receptor tyrosine kinase inhibitors by quantitative structure–activity relationships, molecular dynamics simulation and free energy calculation. RSC Adv 2016. [DOI: 10.1039/c6ra03743g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Employing the combined strategy to understand the features of KDR–ligands complexes, and provide a basis for rational design of inhibitors.
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Affiliation(s)
- Juan Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Xiaorong Wen
- 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
| | - 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
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
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11
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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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12
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Chen YC. Beware of docking! Trends Pharmacol Sci 2015; 36:78-95. [DOI: 10.1016/j.tips.2014.12.001] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/23/2014] [Accepted: 12/02/2014] [Indexed: 12/16/2022]
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13
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Mahto MK, Yellapu NK, Kilaru RB, Chamarthi NR, Bhaskar M. Molecular designing and in silico evaluation of darunavir derivatives as anticancer agents. Bioinformation 2014; 10:221-6. [PMID: 24966524 PMCID: PMC4070053 DOI: 10.6026/97320630010221] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 04/17/2014] [Indexed: 11/23/2022] Open
Abstract
Darunavir is a synthetic nonpeptidic protease inhibitor which has been tested for anticancer properties. To deduce and enhance the anticancer activity of the Darunavir, we have modified its reactive moiety in an effective way. We designed 9 analogues in ChemBioOffice 2010 and minimized using the LigPrep tool of Schrödinger 2011. These analogues can obstruct the activity of other signalling pathways which are implicated in many tumors. Results of the QikProp showed that all the analogues lied in the specified range of all the pharmacokinetic (ADMET) properties required to become the successful drug. Docking study was performed to test its anticancer activity against the biomarkers of the five main types of cancers i.e. bone, brain, breast, colon and skin cancer. Grid was generated for each oncoproteins by specifying the active site amino acids. The binding model of best scoring analogue with each protein was assessed from their G-scores and disclosed by docking analysis using the XP visualizer tool. An analysis of the receptor-ligand interaction studies revealed that these nine Darunavir analogues are active against all cancer biomarkers and have the features to prove themselves as anticancer drugs, further to be synthesized and tested against the cell lines.
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Affiliation(s)
- Manoj kumar Mahto
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, AP, India, 522510
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, AP, India, 517502
| | - Nanda Kumar Yellapu
- Biomedical Informatics Center, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006
| | - Ravendra Babu Kilaru
- Department of Chemistry, Sri Venkateswara University, Tirupati, AP, 517502, India
| | - Naga Raju Chamarthi
- Department of Chemistry, Sri Venkateswara University, Tirupati, AP, 517502, India
| | - Matcha Bhaskar
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, AP, India, 517502
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Ameen D, Snape TJ. Chiral 1,1-diaryl compounds as important pharmacophores. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00088e] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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