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Shaikh SA, Labhade SR, Kale RR, Pachorkar PY, Meshram RJ, Jain KS, Labhade HS, Boraste DR, More RA, Chobe SS, Ballabh D, Wakchaure SN. Synthesis, Biological and Molecular Docking Studies of Thiazole-Thiadiazole derivatives as potential Anti-Tuberculosis Agents. Chem Biodivers 2024:e202400496. [PMID: 38700369 DOI: 10.1002/cbdv.202400496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Tuberculosis remains a global health threat, with increasing infection rates and mortality despite existing anti-TB drugs. The present work focuses on the research findings regarding the development and evaluation of thiadiazole-linked thiazole derivatives as potential anti-tuberculosis agents. We present the synthesis data and confirm the compound structures using spectroscopic techniques. The current study reports twelve thiazole-thiadiazole compounds (5 a-5 l) for their anti-tuberculosis and related bioactivities. This paper emphasizes compounds 5 g, 5 i, and 5 l, which exhibited promising MIC values, leading to further in silico and interaction analysis. Pharmacophore mapping data included in the present analysis identified tubercular ThyX as potential drug targets. The compounds were evaluated for anti-tubercular activity using standard methods, revealing significant MIC values, particularly compound 5 l, with the best MIC value of 7.1285 μg/ml. Compounds 5 g and 5 i also demonstrated moderate to good MIC values against M. tuberculosis (H37Ra). Structural inspection of the docked poses revealed interactions such as hydrogen bonds, halogen bonds, and interactions containing Pi electron cloud, shedding light on conserved interactions with residues like Arg 95, Cys 43, His 69, and Arg 87 from the tubercular ThyX enzyme.
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Affiliation(s)
- Samin A Shaikh
- Department of Chemistry, Kr. V. N. Naik Shikshan Prasarak Sanstha's Arts, Commerce and Science College, Canada Corner, 422002, Nashik, Maharashtra, India
| | - Shivaji R Labhade
- Department of Chemistry, KTHM College, Gangapur Road, 422002, Nashik, Maharashtra, India
| | - Raju R Kale
- Department of Chemistry, KTHM College, Gangapur Road, 422002, Nashik, Maharashtra, India
| | - Prajakta Y Pachorkar
- Department of Microbiology, KTHM College, Gangapur Road, 422002, Nashik, Maharashtra, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, 411007, Pune, Maharashtra, India
| | - Kamlesh S Jain
- Department of Chemistry, Kr. V. N. Naik Shikshan Prasarak Sanstha's Arts, Commerce and Science College, Canada Corner, 422002, Nashik, Maharashtra, India
| | - Hrishikesh S Labhade
- Department of Chemistry, KTHM College, Gangapur Road, 422002, Nashik, Maharashtra, India
| | - Deepak R Boraste
- G. E. Society's, R.N.C Arts, J.D.B Commerce, N.S.C. Science College, Nashik Road, 422101, Nashik, Maharashtra, India
| | - Rahul A More
- Department of Microbiology, Dayanand Science College, 413512, Latur, Maharashtra, India
| | - Santosh S Chobe
- Department of Chemistry, M.G. V's Loknete Vyankatrao Hiray, Arts, Science and Commerce College, Panchavati, 422003, Nashik, Maharashtra, India
| | - Debopriya Ballabh
- Bioinformatics Centre, Savitribai Phule Pune University, 411007, Pune, Maharashtra, India
| | - Satish N Wakchaure
- Department of Synthetic R & D, Delta Finochem Private Limited, Gate No. 350, Village Wadivarhe, Tal-Igatpuri, 422403, Nashik, Maharashtra, India
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More NA, Jadhao NL, Meshram RJ, Tambe P, Salve RA, Sabane JK, Sawant SN, Gajbhiye V, Gajbhiye JM. Novel 3-fluoro-4-morpholinoaniline derivatives: Synthesis and assessment of anti-cancer activity in breast cancer cells. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Lodha KK, Wavhal DS, Bhalekar SB, Meshram RJ, Shinde VS. Exploring New Tetrahydrothienopyridine Derivatives as Platelet Agglutination Inhibitors: Synthesis, Biological Evaluation and In Silico Study. ChemistrySelect 2022. [DOI: 10.1002/slct.202103428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kamlesh K. Lodha
- Department of Chemistry Savitribai Phule Pune University (Formerly University of Pune) Pune 411007 India
| | - Deepak S. Wavhal
- Department of Chemistry Savitribai Phule Pune University (Formerly University of Pune) Pune 411007 India
| | - Sujit B. Bhalekar
- Department of Chemistry S.S.G.M. College Savitribai Phule Pune University (Formerly University of Pune) Kopargaon, Dist-Ahmednagar 423601 India
| | - Rohan J. Meshram
- Bioinformatics Centre Savitribai Phule Pune University Formerly University of Pune) Pune 411007 India
| | - Vaishali S. Shinde
- Department of Chemistry Savitribai Phule Pune University (Formerly University of Pune) Pune 411007 India
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Sawant AS, Kamble SS, Pisal PM, Sawant SS, Hese SV, Bagul KT, Pinjari RV, Kamble VT, Meshram RJ, Gacche RN. Synthesis and evaluation of N-(4-(substituted)-3-(trifluoromethyl) phenyl) isobutyramides and their N-ethyl analogous as anticancer, anti-angiogenic & antioxidant agents: In vitro and in silico analysis. Comput Biol Chem 2021; 92:107484. [PMID: 33865034 DOI: 10.1016/j.compbiolchem.2021.107484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/17/2022]
Abstract
N-(4-(substituted)-3-(trifluoromethyl) phenyl) isobutyramides and their N-ethyl analogues (flutamides) are versatile scaffolds with a wide spectrum of biological activities. A series of new N-(4-(substituted)-3-(trifluoromethyl) phenyl) isobutyramides (8a-t) and their N-ethyl analogous (9a-t) were synthesized and characterized. The inhibitory potential of the synthesized compounds on the viability of three human cancer cell lines HEP3BPN 11 (liver), MDA-MB 453 (breast), and HL 60 (leukemia) were assessed. Among all the compounds 8 L, 8q, 9n and 9p showed higher inhibitory activity on the viability of HL 60 than the standard methotrexate. These lead molecules were then tested for their potential to inhibit the activity of proangiogenic cytokines. The compound 9n showed significantly better inhibition against two cytokines viz. TNFα and Leptin as compared to the standard suramin, while 9p has activity comparable to suramin against IGF1, VEGF, FGFb, and Leptin. The 8q is found to be strong antiangiogenic agent against IGF1, VEGF and TGFβ; while 8 L has showed activity against TNFα, VEGF, and Leptin inhibition. Furthermore antioxidant potential of 8a-t and 9a-t compounds was screened using DPPH, OH and SOR radical scavenging activities. The OH radical scavenging activity of 8c and DPPH activities of 9n as well as 9o are significant as compared to respective standards ascorbic acid and α-tocopherol. The 8c, 9p and 9 h have also exhibited potential antioxidant activity. Additionally, we present in silico molecular docking data to provide the structural rationale of observed TNFα inhibition against newly synthesized compounds. Overall, the synthesized flutamide derivatives have not only anticancer activity, but also possess dual inhibitory effect (anti-angiogenesis and antioxidant) and hence can act as a promising avenue to develop further anticancer agents.
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Affiliation(s)
- Ajay S Sawant
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded-431 606, MS, India
| | - Sonali S Kamble
- Gramin Science (Vocational) College, Vishnupuri, Nanded-431 606, MS, India
| | - Parshuram M Pisal
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded-431 606, MS, India
| | - Sanjay S Sawant
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded-431 606, MS, India
| | - Shrikant V Hese
- DD Bhoyar College of Arts and Science Mouda, Nagpur, 441104, MS, India
| | - Kamini T Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Rahul V Pinjari
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded-431 606, MS, India
| | - Vinod T Kamble
- Organic Chemistry Research Laboratory, Department of Chemistry, Institute of Science, Nagpur, MS, India.
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, MS, India.
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Taksande AM, Gandhi A, Meshram RJ, Gandhi A, Lohakare A. Glioma Presenting as an Isolated Facial Nerve Palsy: A Case Report. Neurol India 2020; 68:900-902. [PMID: 32859838 DOI: 10.4103/0028-3886.293480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
A peripheral palsy of the facial nerve that results in muscle weakness on one side of the face usually manifests as Bell's palsy. Glioma in the left half of the pons and middle cerebellar peduncle is a rare cause of isolated infranuclear facial paralysis. We report a case of 12- year-old female patient who came to our hospital with isolated unilateral facial palsy but turned out to have a low grade glioma.
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Affiliation(s)
- Amar M Taksande
- Department of Pediatrics, Jawaharlaal Nehru Medical College, Sawangi Meghe, Wardha, Maharashtra, India
| | - Akashi Gandhi
- Department of Pediatrics, Jawaharlaal Nehru Medical College, Sawangi Meghe, Wardha, Maharashtra, India
| | - R J Meshram
- Department of Pediatrics, Jawaharlaal Nehru Medical College, Sawangi Meghe, Wardha, Maharashtra, India
| | - Animesh Gandhi
- Department of Pediatrics, Jawaharlaal Nehru Medical College, Sawangi Meghe, Wardha, Maharashtra, India
| | - Amol Lohakare
- Department of Pediatrics, Jawaharlaal Nehru Medical College, Sawangi Meghe, Wardha, Maharashtra, India
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Meshram RJ, Bagul KT, Aouti SU, Shirsath AM, Duggal H, Gacche RN. Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. Mol Divers 2020; 25:1679-1700. [PMID: 32737682 DOI: 10.1007/s11030-020-10129-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/22/2020] [Indexed: 01/16/2023]
Abstract
Leishmaniasis is one of the most neglected tropical diseases that demand immediate attention to the identification of new drug targets and effective drug candidates. The present study demonstrates the possibility of using threonine synthase (TS) as a putative drug target in leishmaniasis disease management. We report the construction of an effective homology model of the enzyme that appears to be structurally as well as functionally well conserved. The 200 nanosecond molecular dynamics data on TS with and without pyridoxal phosphate (PLP) shed light on mechanistic details of PLP-induced conformational changes. Moreover, we address some important structural and dynamic interactions in the PLP binding region of TS that are in good agreement with previously speculated crystallographic estimations. Additionally, after screening more than 44,000 compounds, we propose 10 putative inhibitor candidates for TS based on virtual screening data and refined Molecular Mechanics Generalized Born Surface Area calculations. We expect that structural and functional dynamics data disclosed in this study will help initiate experimental endeavors toward establishing TS as an effective antileishmanial drug target.
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Affiliation(s)
- Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India.
| | - Kamini T Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Snehal U Aouti
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Akshay M Shirsath
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Harleen Duggal
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
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Meshram RJ, Shirsath A, Aouti S, Bagul K, Gacche RN. Molecular modeling and simulation study of homoserine kinase as an effective leishmanial drug target. J Mol Model 2020; 26:218. [PMID: 32720228 DOI: 10.1007/s00894-020-04473-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/14/2020] [Indexed: 11/25/2022]
Abstract
Leishmaniasis is a tropical neglected disease that imposes major health concerns in many endemic countries worldwide and requires urgent attention to the identification of new drug targets as well as drug candidates. In the current study, we propose homoserine kinase (HSK) inhibition as a strategy to induce pathogen mortality via generating threonine deficiency. We introduce a homology-based molecular model of leishmanial HSK that appears to possess all conserved structural as well as functional features in the GHMP kinase family. Furthermore, 200 ns molecular dynamics data of the enzyme in open and closed state attempts to provide the mechanistic details involved in the substrate as well as phosphate binding to this enzyme. We discuss the structural and functional significance of movements involved in various loops (motif 1, 2, 3) and lips (upper and lower) in the transition of leishmanial HSK from closed to open state. Virtual screening data of more than 40,000 compounds from the present investigation tries to identify a few potential HSK inhibitors that possess important features to act as efficient HSK inhibitors. These compounds can be considered an effective starting point for the identification of novel drug-like scaffolds. We hope the structural wealth that is offered in this report will be utilized in designing competent experimental and therapeutic interventions for leishmaniasis management. Graphical abstract.
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Affiliation(s)
- Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India.
| | - Akshay Shirsath
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Snehal Aouti
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Kamini Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
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8
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Sawant AS, Kamble SS, Pisal PM, Meshram RJ, Sawant SS, Kamble VA, Kamble VT, Gacche RN. Synthesis and evaluation of a novel series of 6-bromo-1-cyclopentyl-1H-indazole-4-carboxylic acid-substituted amide derivatives as anticancer, antiangiogenic, and antioxidant agents. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02454-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Kolte BS, Londhe SR, Bagul KT, Pawnikar SP, Goundge MB, Gacche RN, Meshram RJ. FlavoDb: a web-based chemical repository of flavonoid compounds. 3 Biotech 2019; 9:431. [PMID: 31696036 DOI: 10.1007/s13205-019-1962-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022] Open
Abstract
There are many online resources that focus on chemical diversity of natural compounds, but only handful of resources exist that focus solely on flavonoid compounds and integrate structural and functional properties; however, extensive collated flavonoid literature is still unavailable to scientific community. Here we present an open access database 'FlavoDb' that is focused on providing physicochemical properties as well as topological descriptors that can be effectively implemented in deducing large scale quantitative structure property models of flavonoid compounds. In the current version of database, we present data on 1, 19,400 flavonoid compounds, thereby covering most of the known structural space of flavonoid class of compounds. Moreover, effective structure searching tool presented here is expected to provide an interactive and easy-to-use tool for obtaining flavonoid-based literature and allied information. Data from FlavoDb can be freely accessed via its intuitive graphical user interface made available at following web address: http://bioinfo.net.in/flavodb/home.html.
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Hartung F, Patil A, Meshram RJ, Weber GF. Gene expression signatures of site-specificity in cancer metastases. Clin Exp Metastasis 2019; 37:159-171. [PMID: 31555944 DOI: 10.1007/s10585-019-09995-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/19/2019] [Indexed: 11/26/2022]
Abstract
We have previously shown that metastases are generally characterized by a core program of gene expression that induces the oxidative energy metabolism, activates vascularization/tissue remodeling, silences extracellular matrix interactions, and alters ion homeostasis. This core program distinguishes metastases from their originating primary tumors as well as from their target host tissues. We hypothesized that organ preference is reflected in additional, site-selective components within the metastatic gene expression programs. Expanding our prior analysis of 653 human gene expression profiles plus data from a murine model, we find that the release from the primary tumor is associated with a suppression of functions that are important for the identity of the organ of origin, such as a down-regulation of steroid hormone responsiveness in the disseminated foci derived from prostate cancer. Metastases adjust to their target microenvironment by up-regulating-even overexpressing-genes and genetic programs that are characteristic of that organ. Finally, alterations in RNA and protein processing as well as immune deviation are common. In the clinic, metastases are mostly treated with the chemotherapy protocols devised for their primary tumors. Adjustments that account for the gene expression differences between primary and metastatic cancers have the potential to improve the currently dismal success rates.
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Affiliation(s)
- Franz Hartung
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA
| | - Aditya Patil
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Georg F Weber
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA.
- James L. Winkle College of Pharmacy, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH, 45267-0514, USA.
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Meshram RJ, Bagul KT, Pawnikar SP, Barage SH, Kolte BS, Gacche RN. Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities. J Biomol Struct Dyn 2019; 38:1168-1184. [DOI: 10.1080/07391102.2019.1597770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rohan J. Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Kamini T. Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Shristi P. Pawnikar
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sagar H. Barage
- Amity Institute of Biotechnology, Amity University, Panvel, Maharashtra, India
| | - Baban S. Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N. Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
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Ambhore AN, Kamble SS, Kadam SN, Kamble RD, Hebade MJ, Hese SV, Gaikwad MV, Meshram RJ, Gacche RN, Dawane BS. Design, synthesis and in silico study of pyridine based 1,3,4-oxadiazole embedded hydrazinecarbothioamide derivatives as potent anti-tubercular agent. Comput Biol Chem 2019; 80:54-65. [PMID: 30901601 DOI: 10.1016/j.compbiolchem.2019.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 12/15/2022]
Abstract
Development of novel, safe and effective drug candidates combating the emerging drug resistance has remained a major focus in the mainstream of anti-tuberculosis research. Here, we inspired to design and synthesize series of new pyridin-4-yl-1,3,4-oxadiazol-2-yl-thio-ethylidene-hydrazinecarbothioamide derivatives as potential anti-tubercular agents. The anti-tubercular bioactive assay demonstrated that the synthesized compounds exhibit potent anti-tubercular activity (MIC = 3.9-7.81 μg/mL) in comparison with reference drugs Rifampicin and Isoniazid.We employed pharmacophore probing approach for the identification of CYP51 as a possible drug target for the synthesized compounds. To understand the preferable binding mode, the synthesized molecules were docked onto the active site of Sterol 14 α-demethylases (CYP51) target. From the binding free energy of the docking results it was revealed that the compounds were effective CYP51 inhibitors and acts as antitubercular agent.
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Affiliation(s)
- Ajay N Ambhore
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Sonali S Kamble
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Shuddhodan N Kadam
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Rahul D Kamble
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Madhav J Hebade
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Shrikant V Hese
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Milind V Gaikwad
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411 007, India.
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, MS, 411 007, India.
| | - Bhaskar S Dawane
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India.
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Patil KK, Meshram RJ, Barage SH, Gacche RN. Dietary flavonoids inhibit the glycation of lens proteins: implications in the management of diabetic cataract. 3 Biotech 2019; 9:47. [PMID: 30729071 DOI: 10.1007/s13205-019-1581-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
The intervention of functional foods as complementary therapeutic approach for the amelioration of diabetes and sugar induced cataractogenesis is more appreciated over the present day chemotherapy agents owing to their nontoxic and increased bioavailability concerns. Dietary flavonoids, a class of bioactive phytochemicals is known to have wide range of biological activities against variety of human ailments. In the present study, we demonstrate anti-cataract effect of eight dietary flavonoids in sugar induced lens organ culture study. We present data on processes like inhibition of glycation-induced lens cloudiness, lens protein aggregation, glycation reaction and advanced glycation end products formation that can act as biochemical markers for this disease. The selected flavonoids were also tested for their aldose reductase (AR) inhibition (experimental and in silico). The molecular dynamics simulation results shed light on mechanistic details of flavonoid induced AR inhibition. The outcome of the present study clearly focuses the significance of kaempferol, taxifolin and quercetin as potential candidates for controlling diabetic cataract.
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Affiliation(s)
- Kapil K Patil
- 1School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS 431 606 India
| | - Rohan J Meshram
- 2Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS 411007 India
| | - Sagar H Barage
- 2Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS 411007 India
- 4Amity Institute of Biotechnology, Amity University, Panvel, MS India
| | - Rajesh N Gacche
- 1School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS 431 606 India
- 3Department of Biotechnology, Savitribai Phule Pune University, Pune, MS 411007 India
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14
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Meshram RJ, Goundge MB, Kolte BS, Gacche RN. An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitol Int 2018; 69:59-70. [PMID: 30503238 DOI: 10.1016/j.parint.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022]
Abstract
Leishmaniasis is one of the major health issue in developing countries. The current therapeutic regimen for this disease is less effective with lot of adverse effects thereby warranting an urgent need to develop not only new and selective drug candidates but also identification of effective drug targets. Here we present subtractive genomics procedure for identification of putative drug targets in Leishmania. Comprehensive druggability analysis has been carried out in the current work for identified metabolic pathways and drug targets. We also demonstrate effective metabolic simulation methodology to pinpoint putative drug targets in threonine biosynthesis pathway. Metabolic simulation data from the current study indicate that decreasing flux through homoserine kinase reaction can be considered as a good therapeutic opportunity. The data from current study is expected to show new avenue for designing experimental strategies in search of anti-leishmanial agents.
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Affiliation(s)
- Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
| | - Mayuri B Goundge
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Baban S Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
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Kolte BS, Londhe SR, Solanki BR, Gacche RN, Meshram RJ. FilTer BaSe: A web accessible chemical database for small compound libraries. J Mol Graph Model 2018; 80:95-103. [PMID: 29328995 DOI: 10.1016/j.jmgm.2017.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 12/11/2022]
Abstract
Finding novel chemical agents for targeting disease associated drug targets often requires screening of large number of new chemical libraries. In silico methods are generally implemented at initial stages for virtual screening. Filtering of such compound libraries on physicochemical and substructure ground is done to ensure elimination of compounds with undesired chemical properties. Filtering procedure, is redundant, time consuming and requires efficient bioinformatics/computer manpower along with high end software involving huge capital investment that forms a major obstacle in drug discovery projects in academic setup. We present an open source resource, FilTer BaSe- a chemoinformatics platform (http://bioinfo.net.in/filterbase/) that host fully filtered, ready to use compound libraries with workable size. The resource also hosts a database that enables efficient searching the chemical space of around 348,000 compounds on the basis of physicochemical and substructure properties. Ready to use compound libraries and database presented here is expected to aid a helping hand for new drug developers and medicinal chemists.
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Affiliation(s)
- Baban S Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Sanjay R Londhe
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | | | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India.
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Meshram RJ, Baladhye VB, Gacche RN, Karale BK, Gaikar RB. Pharmacophore Mapping Approach for Drug Target Identification: A Chemical Synthesis and in Silico Study on Novel Thiadiazole Compounds. J Clin Diagn Res 2017; 11:KF01-KF08. [PMID: 28658808 DOI: 10.7860/jcdr/2017/22761.9925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/23/2016] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Compounds containing thiadiazole moiety are cognized to possess with variety of clinical and therapeutic activity. Finding a suitable drug target for newly synthesized compounds remain a major bottle neck in current high throughout medicinal chemistry era. AIM To effectively synthesize di substituted thiadiazole compounds and demonstrate drug target identification using an in silico pharmacophore probing approach. Moreover, we also aim to validate the suitability of identified drug target. MATERIALS AND METHODS A cost-effective and environmental friendly chemical synthesis scheme for production of di substituted thiadiazole compounds was employed. Target identification was conducted by Pharmmapper software. Validation was accomplished by performing molecular docking and further Molecular Hydrophobic Potential (MHP) analysis. RESULTS Pharmacophore probing base approach identified hepatocyte growth factor receptor (c-Met) as a suitable biological target for newly synthesized compounds. Binding free energy values indicate that compound 4b, 4e, 4g and 4h has tremendous potential to be further used as lead compound to design selective inhibitors of c-Met receptor. MHP data from current study supports the possibility that hydrophobic contacts might act as major factor stabilizing thiadiazole- c-Met complex. Moreover, in silico observations of current study are in absolute accordance with previously described in vitro and crystallographic analysis. CONCLUSION We demonstrate that thiadiazole compounds synthesized in current investigation has high potential to act in modulation of hepatocyte growth factor receptor (c-Met) activity and thereby act as putative therapeutic agent in cancer therapy.
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Affiliation(s)
- Rohan J Meshram
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Vijay B Baladhye
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N Gacche
- Professor, Department of Botany, School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Bhausaheb K Karale
- Professor, Department of Chemistry, Radhabai Kale Mahila Mahavidayalaya, Ahmednagar, Maharashtra, India
| | - Rajendra B Gaikar
- Assistant Professor, Department of Chemistry, Padmashri Vikhe Patil College, Loni, Maharashtra, India
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Patil KK, Meshram RJ, Gacche RN. Effect of monohydroxylated flavonoids on glycation-induced lens opacity and protein aggregation. J Enzyme Inhib Med Chem 2016; 31:148-156. [DOI: 10.1080/14756366.2016.1180593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Kapil K. Patil
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Rohan J. Meshram
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Rajesh N. Gacche
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
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Mogle PP, Meshram RJ, Hese SV, Kamble RD, Kamble SS, Gacche RN, Dawane BS. Synthesis and molecular docking studies of a new series of bipyrazol-yl-thiazol-ylidene-hydrazinecarbothioamide derivatives as potential antitubercular agents. Med Chem Commun 2016. [DOI: 10.1039/c6md00085a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Substituted 2-(2-(5-(3/4-substituted phenyl)-4-hydroxy-3′-(3/4-substituted phenyl)-1′-phenyl-1H,1′H-[3,4′-bipyrazol]-1-yl)thiazol-4(5H)ylidene) hydrazinecarbothioamide derivatives have been synthesized in good yields by an efficient method.
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Affiliation(s)
- Pratima P. Mogle
- School of Chemical Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India 431606
| | - Rohan J. Meshram
- School of Life Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India
| | - Shrikant V. Hese
- School of Chemical Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India 431606
| | - Rahul D. Kamble
- School of Chemical Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India 431606
| | - Sonali S. Kamble
- School of Life Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India
| | - Rajesh N. Gacche
- School of Life Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India
| | - Bhaskar S. Dawane
- School of Chemical Sciences
- Swami Ramanand Teerth Marathwada University
- Nanded (MS)
- India 431606
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Shaikh RU, Dawane AA, Pawar RP, Gond DS, Meshram RJ, Gacche RN. Inhibition of Helicobacter pylori
and Its Associate Urease by Labdane Diterpenoids Isolated from Andrographis paniculata. Phytother Res 2015; 30:412-7. [DOI: 10.1002/ptr.5542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Rafik U. Shaikh
- Department of Botany; Poona College; Camp Pune 411 001 MS India
| | - Ashwini A. Dawane
- School of Life Sciences; Swami Ramanand Teerth Marathwada University; Nanded 431 606 MS India
| | - Rajendra P. Pawar
- Department of Chemistry; Deogiri College; Aurangabad 431 005 MS India
| | - Dhananjay S. Gond
- Department of Microbiology; Savitribai Phule Pune University; Pune 411 007 MS India
| | - Rohan J. Meshram
- School of Life Sciences; Swami Ramanand Teerth Marathwada University; Nanded 431 606 MS India
| | - Rajesh N. Gacche
- School of Life Sciences; Swami Ramanand Teerth Marathwada University; Nanded 431 606 MS India
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Meshram RJ, Gacche RN. Effective epitope identification employing phylogenetic, mutational variability, sequence entropy, and correlated mutation analysis targeting NS5B protein of hepatitis C virus: from bioinformatics to therapeutics. J Mol Recognit 2015; 28:492-505. [PMID: 25727409 DOI: 10.1002/jmr.2466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 11/21/2014] [Accepted: 01/16/2015] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV) is considered as a foremost cause affecting numerous human liver-related disorders. An effective immuno-prophylactic measure (like stable vaccine) is still unavailable for HCV. We perform an in silico analysis of nonstructural protein 5B (NS5B) based CD4 and CD8 epitopes that might be implicated in improvement of treatment strategies for efficient vaccine development programs against HCV. Here, we report on effective utilization of knowledge obtained from multiple sequence alignment and phylogenetic analysis for investigation and evaluation of candidate epitopes that have enormous potential to be used in formulating proficient vaccine, embracing multiple strains prevalent among major geographical locations. Mutational variability data discussed herein focus on discriminating the region under active evolutionary pressure from those having lower mutational potential in existing experimentally verified epitopes, thus, providing a concrete framework for designing an effective peptide-based vaccine against HCV. Additionally, we measured entropy distribution in NS5B residues and pinpoint the positions in epitopes that are more susceptible to mutations and, thus, account for virus strategy to evade the host immune system. Findings from this study are expected to add more details on the sequence and structural aspects of NS5B protein, ultimately facilitating our understanding about the pathophysiology of HCV and assisting advance studies on the function of NS5B antigen on the epitope level. We also report on the mutational crosstalk between functionally important coevolving residues, using correlated mutation analysis, and identify networks of coupled mutations that represent pathways of allosteric communication inside and among NS5B thumb, finger, and palm domains.
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Gacche RN, Shegokar HD, Gond DS, Meshram RJ. Abstract 1006: Structural peculiarities of flavonoids influence anti-angiogenic, cytotoxic and antioxidant effects: experimental and insilico analysis. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-1006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Structural diversity of flavonoids and biological activities has remained an important discourse in the mainstream of flavonoid research. In the present studies different class of flavonoids such as flavones, flavanones and flavanolols were evaluated for their antiangiogenic, cytotoxic and antioxidant activities. The anti-angiogenic activity was evaluated using in vivo chorioallantoic membrane model (CAM), antioxidant potential and kinetics of free radical scavenging activity was determined using DPPH (2, 2-diphenyl-1-picryl hydrazine) and superoxide anion radical (SOR) scavenging assays, while cytotoxicity against selected cancer cell lines was carried out using MTT cell viability assay. The physicochemical properties/quantum chemical discriptors of the selected flavonoids were calculated using BioMed CAChe 6.1.10 drug. The selected flavonoids were docked in silico onto the proangiogenic peptides such as vascular endothelial growth factor (VEGF), hypoxia inducible factor (HIF-1α), and vascular endothelial growth factor receptor-2 (VEGFR2) and others from human origin. The results of the present investigation are discussed in the mainstream of structure activity relationship which may be useful in translating flavonoids as therapeutic molecules targeting angiogenesis.
References
1. Gacche R. N. Shegokar Harshala, Gond Dhananjay , A. D. Jadhav and Ghole Vikram. (2010). Effect of Hydroxyl Substitution of Flavone on Antiangiogenic and Free Radical Scavenging Activities: A Structure Activity Relationship Studies Using Computational Tools. European J. Pharmaceutical Science 39, 37-44.
2. Gacche R. N. Shegokar Harshala, Gond Dhananjay , Zhenzhou Yang, A. D. Jadhav (2011). Evaluation of selected flavonoids as antiangiogenic, anticancer and radical scavenging agents: an experimental and in silico analysis. Cell Biochemistry and Biophysics 61, 651-663. DOI 10.1007/s12013-011-9252-z.
3. Gacche RN and Meshram RJ (2013) Targeting Tumor Micro-environment for Design and Development of Novel Anti-angiogenic Agents Arresting Tumor Growth. Progress in Biophysics & Molecular Biology 113 (2013) 333-354.
Note: This abstract was not presented at the meeting.
Citation Format: Raju N. Gacche, Harshala D. Shegokar, Dhananjay S. Gond, Rohan J. Meshram. Structural peculiarities of flavonoids influence anti-angiogenic, cytotoxic and antioxidant effects: experimental and insilico analysis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1006. doi:10.1158/1538-7445.AM2014-1006
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Kamble RD, Hese SV, Meshram RJ, Kote JR, Gacche RN, Dawane BS. Green synthesis and in silico investigation of dihydro-2H-benzo[1,3]oxazine derivatives as inhibitors of Mycobacterium tuberculosis. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1165-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gacche RN, Meshram RJ. Angiogenic factors as potential drug target: Efficacy and limitations of anti-angiogenic therapy. Biochim Biophys Acta Rev Cancer 2014; 1846:161-79. [DOI: 10.1016/j.bbcan.2014.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022]
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Bandgar BP, Adsul LK, Chavan HV, Jalde SS, Shringare SN, Shaikh R, Meshram RJ, Gacche RN, Masand V. Synthesis, biological evaluation, and docking studies of 3-(substituted)-aryl-5-(9-methyl-3-carbazole)-1H-2-pyrazolines as potent anti-inflammatory and antioxidant agents. Bioorg Med Chem Lett 2012; 22:5839-44. [PMID: 22901385 DOI: 10.1016/j.bmcl.2012.07.080] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/06/2012] [Accepted: 07/24/2012] [Indexed: 11/24/2022]
Abstract
A novel series of 3-(substituted)-aryl-5-(9-methyl-3-carbazole)-1H-2-pyrazolines (5a-o) has been synthesized and the structures of newly synthesized compounds were characterized by IR, (1)H NMR and mass spectral analysis. All the synthesized compounds were evaluated for their in vitro and in vivo anti-inflammatory activity, and also for their antioxidant activity. Compounds 5b, 5c, 5d and 5n were found to be selective COX-2 inhibitors. Compound 5c was found to potent inhibitor of the carrageenin induced paw edema in rats. Most of the compounds exhibited good DPPH and superoxide radical scavenging activity, while compounds 5c, 5d, 5i and 5k exhibited good hydroxyl radical scavenging activity. Molecular docking result, along with the biological assay data, suggested that compound 5c was a potential anti-inflammatory agent.
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Affiliation(s)
- Babasaheb P Bandgar
- Medicinal Chemistry Research Laboratory, School of Chemical Sciences, Solapur University, Solapur 413 255, Maharashtra, India.
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Meshram RJ, Gavhane A, Gaikar R, Bansode T, Maskar A, Gupta A, Sohni S, Patidar M, Pandey T, Jangle S. Sequence analysis and homology modeling of laccase from Pycnoporus cinnabarinus. Bioinformation 2010; 5:150-4. [PMID: 21364777 PMCID: PMC3040475 DOI: 10.6026/97320630005150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/26/2010] [Indexed: 11/30/2022] Open
Abstract
Industrial effluents of textile, paper, and leather industries contain various toxic dyes as one of the waste material. It imparts major impact on human
health as well as environment. The white rot fungus Pycnoporus cinnabarinus Laccase is generally used to degrade these toxic dyes. In order to decipher
the mechanism of process by which Laccase degrade dyes, it is essential to know its 3D structure. Homology modeling was performed in presented work,
by satisfying Spatial restrains using Modeller Program, which is considered as standard in this field, to generate 3D structure of Laccase in unison,
SWISSMODEL web server was also utilized to generate and verify the alternative models. We observed that models created using Modeller stands better
on structure evaluation tests. This study can further be used in molecular docking techniques, to understand the interaction of enzyme with its mediators
like 2, 2‐azinobis (3‐ethylbenzthiazoline‐6‐sulfonate) (ABTS) and Vanillin that are known to enhance the Laccase activity.
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Affiliation(s)
- Rohan J Meshram
- Center for Biotechnology, Pravara Institute of Medical Sciences, Loni, Taluka: Rahata, District: Ahmednagar, Maharashtra, India
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