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Patel VK, Rajak H. Structural Investigations of Aroylindole Derivatives through 3D-QSAR and Multiple Pharmacophore Modeling for the Search of Novel Colchicines Inhibitor. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200905092444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background :
The ligand and structure based integrated strategies are being repeatedly
and effectively employed for the precise search and design of novel ligands against various disease
targets. Aroylindole derivative has a similar structural analogy as Combretastatin A-4, and exhibited
potent anticancer activity on several cancer cell lines.
Objective:
To identify structural features of aroylindole derivatives through 3D-QSAR and multiple
pharmacophore modelling for the search of novel colchicines inhibitor via virtual screening.
Method:
The present study utilizes ligand and structure based methodology for the establishment
of structure activity correlation among trimethoxyaroylindole derivatives and the search of novel
colchicines inhibitor via virtual screening. The 3D-QSAR studies were performed using Phase module
and provided details of relationship between structure and biological activity. A single ligand
based pharmacophore model was generated from Phase on compound 3 and compound 29 and three
energetically optimized structure based pharmacophore models were generated from epharmacophore
for co-crystallized ligand, compound 3 and compound 29 with protein PBD ID
1SA0, 5EYP and 5LYJ. These pharmacophoric features containing hit-like compounds were collected
from commercially available ZINC database and screened using virtual screening workflow.
Results and Discussion:
The 3D-QSAR model studies with good PLSs statistics for factor four was
characterized by the best prediction coefficient Q2 (0.8122), regression R2 (0.9405), SD (0.2581), F
(102.7), P (1.56e-015), RMSE (0.402), Stability (0.5411) and Pearson-r (0.9397). The generated epharmacophores
have GH scores over 0.5 and AUAC ≥ 0.7 indicated that all the pharmacophores
were suitable for pharmacophore-based virtual screening. The virtual screened compounds
ZINC12323179, ZINC01642724, and ZINC14238006 have showed similar structural alignment as
co-crystallized ligand and showed the hydrogen bonding of ligand with ASN101, SER178,
THR179, VAL238, CYS241 amino acid of protein.
Conclusion:
The study illustrates that the ligand and structure based pharmacophoric approach is
beneficial for identification of structurally diverse hits, having better binding affinity on colchicines
binding site as novel anticancer agents.
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Affiliation(s)
- Vijay Kumar Patel
- Medicinal Chemistry Research Laboratory, SLT Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur 495 009, (C.G.), India
| | - Harish Rajak
- Medicinal Chemistry Research Laboratory, SLT Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur 495 009, (C.G.), India
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Sakle NS, More SA, Mokale SN. A network pharmacology-based approach to explore potential targets of Caesalpinia pulcherima: an updated prototype in drug discovery. Sci Rep 2020; 10:17217. [PMID: 33057155 PMCID: PMC7560621 DOI: 10.1038/s41598-020-74251-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/28/2020] [Indexed: 01/19/2023] Open
Abstract
Caesalpinia pulcherima (CP) is a traditional herb used for the treatment of asthma, bronchitis, cancer, anti-bacterial, anti-fungal and as abortifacient. In the present study, bioactive components and potential targets in the treatment of breast cancer validated through in silico, in vitro and in vivo approach. The results for the analysis were as among 29 components, only four components were found active for further study which proved the use of CP as a multi-target herb for betterment of clinical uses. The results found by PPI states that our network has significant interactions which include the ESR-1, ESR-2, ESRRA, MET, VEGF, FGF, PI3K, PDK-1, MAPK, PLK-1, NEK-2, and GRK. Compound-target network involves 4 active compound and 150 target genes which elucidate the mechanisms of drug action in breast cancer treatment. Furthermore, on the basis of the above results the important proteins were fetched for the docking study which helps in predicting the possible interaction between components and targets. The results of the western blotting showed that CP regulates ER and EGFR expression in MCF-7 cell. In addition to this animal experimentation showed that CP significantly improved immunohistological status in MNU induced carcinoma rats. Network pharmacology approach not only helps us to confirm the study of the chosen target but also gave an idea of compound-target network as well as pathways associated to the CP for treating the complex metabolic condition as breast cancer and they importance for experimental verification.
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Affiliation(s)
- Nikhil S Sakle
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, Maharashtra, 431001, India
| | - Shweta A More
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, Maharashtra, 431001, India
| | - Santosh N Mokale
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, Maharashtra, 431001, India.
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Mokale S, Sakle N, Lokwani D. Caesalpinia pulcherrima sarrests cell cycle and triggers reactive oxygen species-induced mitochondrial-mediated apoptosis and necroptosis via modulating estrogen and estrogen receptors. Pharmacogn Mag 2019. [DOI: 10.4103/pm.pm_100_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Combretastatin A-4 based thiophene derivatives as antitumor agent: Development of structure activity correlation model using 3D-QSAR, pharmacophore and docking studies. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2017. [DOI: 10.1016/j.fjps.2017.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Lokwani D, Azad R, Sarkate A, Reddanna P, Shinde D. Structure Based Library Design (SBLD) for new 1,4-dihydropyrimidine scaffold as simultaneous COX-1/COX-2 and 5-LOX inhibitors. Bioorg Med Chem 2015; 23:4533-4543. [DOI: 10.1016/j.bmc.2015.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 12/27/2022]
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6
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Novel tetrahydropyrimidine–adamantane hybrids as anti-inflammatory agents: synthesis, structure and biological evaluation. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1332-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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7
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Sarkate AP, Murumkar PR, Lokwani DK, Kandhare AD, Bodhankar SL, Shinde DB, Bothara KG. Design of selective TACE inhibitors using molecular docking studies: Synthesis and preliminary evaluation of anti-inflammatory and TACE inhibitory activity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:905-923. [PMID: 26588187 DOI: 10.1080/1062936x.2015.1095240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tumor necrosis factor-α (TNF-α) converting enzyme (TACE) has been considered one of the principal therapeutic targets for the treatment of TNF-dependent pathologies. Several TACE inhibitors have been reported, but none of them has been successfully passed to phase II clinical trials. In the present work, we attempted to design highly selective new non-hydroxamate sulfonamide TACE inhibitors. The docking study was performed on one of the crystal structures of TACE, selected based on its resolution and R value, to tackle the flexibility issue of the active site. The results allowed us to distinguish the analogues with a higher binding affinity toward the active site of TACE and to identify the substituent of analogues needed for binding with the surrounding site of the enzyme. Finally the analogues were docked on crystal structures of six different matrix metalloproteinases (MMPs) for a selectivity study of TACE over MMPs. Some of these analogues were synthesized and subjected to preliminary testing for in vivo anti-inflammatory activity and TACE inhibitory activity.
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Affiliation(s)
- A P Sarkate
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
| | - P R Murumkar
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
| | - D K Lokwani
- b Department of Chemical Technology , Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - A D Kandhare
- c Department of Pharmacology , Poona College of Pharmacy, Bharati Vidyapeeth Deemed University , Pune , Maharashtra , India
| | - S L Bodhankar
- c Department of Pharmacology , Poona College of Pharmacy, Bharati Vidyapeeth Deemed University , Pune , Maharashtra , India
| | - D B Shinde
- b Department of Chemical Technology , Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - K G Bothara
- a Department of Pharmaceutical Chemistry , Sinhgad Institute of Pharmacy , Pune , Maharashtra , India
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Kalva S, Vinod D, Saleena LM. Combined structure- and ligand-based pharmacophore modeling and molecular dynamics simulation studies to identify selective inhibitors of MMP-8. J Mol Model 2014; 20:2191. [DOI: 10.1007/s00894-014-2191-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
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Sośnicki JG, Struk Ł, Kurzawski M, Perużyńska M, Maciejewska G, Droździk M. Regioselective synthesis of novel 4,5-diaryl functionalized 3,4-dihydropyrimidine-2(1H)-thiones via a non-Biginelli-type approach and evaluation of their in vitro anticancer activity. Org Biomol Chem 2014; 12:3427-40. [PMID: 24752551 DOI: 10.1039/c4ob00094c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An easy and novel approach to synthesize 4,5-diaryl functionalized 3,4-dihydropyrimidine-2(1H)-thiones via addition of aryllithiums to 5-aryl substituted pyrimidine-2(1H)-thiones, which could be regarded as a method complementary to the most widely used Biginelli-type synthesis, is described. In the reaction of aryllithiums with N-(Me)Bn substituted pyrimidine-2(1H)-thiones a high degree of regioselectivity of addition, leading to 4-aryl adducts, was achieved. Selected compounds tested for their in vitro anticancer activity against four human cancer cell lines showed the greatest activity against breast cancer (MCF7). 1-Benzyl-4-(3-hydroxyphenyl)-5-phenyl substituted 3,4-dihydropyrimidine-2(1H)-thione (10g) exhibiting 10-fold more potent activity than the best known monastrol (MON) stands as a promising candidate for further scaffold and asymmetric synthesis.
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Affiliation(s)
- Jacek G Sośnicki
- Institute of Chemistry and Environmental Protection, West Pomeranian University of Technology, Szczecin, Al. Piastów 42, Szczecin, 71-065 Poland.
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Bagherzadeh K, Shirgahi Talari F, Sharifi A, Ganjali MR, Saboury AA, Amanlou M. A new insight into mushroom tyrosinase inhibitors: docking, pharmacophore-based virtual screening, and molecular modeling studies. J Biomol Struct Dyn 2014; 33:487-501. [PMID: 24601849 DOI: 10.1080/07391102.2014.893203] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Tyrosinase, a widely spread enzyme in micro-organisms, animals, and plants, participates in two rate-limiting steps in melanin formation pathway which is responsible for skin protection against UV lights' harm whose functional deficiency result in serious dermatological diseases. This enzyme seems to be responsible for neuromelanin formation in human brain as well. In plants, the enzyme leads the browning pathway which is commonly observed in injured tissues that is economically very unfavorable. Among different types of tyrosinase, mushroom tyrosinase has the highest homology with the mammalian tyrosinase and the only commercial tyrosinase available. In this study, ligand-based pharmacophore drug discovery method was applied to rapidly identify mushroom tyrosinase enzyme inhibitors using virtual screening. The model pharmacophore of essential interactions was developed and refined studying already experimentally discovered potent inhibitors employing Docking analysis methodology. After pharmacophore virtual screening and binding modes prediction, 14 compounds from ZINC database were identified as potent inhibitors of mushroom tyrosinase which were classified into five groups according to their chemical structures. The inhibition behavior of the discovered compounds was further studied through Classical Molecular Dynamic Simulations and the conformational changes induced by the presence of the studied ligands were discussed and compared to those of the substrate, tyrosine. According to the obtained results, five novel leads are introduced to be further optimized or directly used as potent inhibitors of mushroom tyrosinase.
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Affiliation(s)
- Kowsar Bagherzadeh
- a Department of Medicinal Chemistry, Faculty of Pharmacy and Medicinal Plants Research Center , Tehran University of Medical Sciences , Tehran , Iran
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Lokwani DK, Mokale SN, Shinde DB. 3D QSAR studies based in silico screening of 4,5,6-triphenyl-1,2,3,4-tetrahydropyrimidine analogs for anti-inflammatory activity. Eur J Med Chem 2014; 73:233-42. [DOI: 10.1016/j.ejmech.2013.10.083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/16/2013] [Accepted: 10/21/2013] [Indexed: 11/26/2022]
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Kalva S, Saranyah K, Suganya PR, Nisha M, Saleena LM. Potent inhibitors precise to S1' loop of MMP-13, a crucial target for osteoarthritis. J Mol Graph Model 2013; 44:297-310. [PMID: 23938376 DOI: 10.1016/j.jmgm.2013.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/21/2013] [Accepted: 06/23/2013] [Indexed: 11/30/2022]
Abstract
Matrix metalloproteinase-13 (MMP-13) is the primary MMP involved in cartilage degradation through its particular ability to cleave type-II collagen. This protein is expressed by chondrocytes and synovial cells in human osteoarthritis and rheumatoid arthritis; hence, it is an attractive target for the treatment of arthritic diseases. Currently available inhibitors lack specificity for metalloproteinase because of a common Zn binding site in MMPs; thus, there is a need to identify selective MMP-13 inhibitors for osteoarthritis therapy. Because selectivity is the major concern, both ligand-based and protein-based pharmacophore methodologies were used to identity potent and selective MMP-13 inhibitors. Different hypotheses were validated, and the best hypothesis was used to screen Zinc (natural and chemical) databases to seek novel scaffolds as MMP-13 inhibitors. The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC). In addition, potent inhibitors were selected based on two criteria: a similar binding mode as that of the active site PB3 crystal ligand and crucial amino acid interactions that are catalytically important for the function of MMP-13. The candidate potent inhibitors ZINC 02535232, ZINC 08399795, ZINC 12419118 and ZINC 00624580 nearly reproduced the H-bond interactions formed in the crystal structure of 1XUC with reasonable RMSD values exhibiting a novel interaction pattern that was not previously observed in MMP-13 inhibitors. The identified potent hits with diverse chemical scaffolds may be useful in designing new MMP-13 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, SRM Nagar, Kattankulathur, Kancheepuram District, Chennai 603203, India
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3D-QSAR and docking studies of benzoyl urea derivatives as tubulin-binding agents for antiproliferative activity. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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