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Nath A, Kumer A, Zaben F, Khan MW. Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00117-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
2,3-Dihydrobenzofurans (DHB) have proposed as advantages structures, and used as chemical entresol to design small compound libraries. The present study illustrates to explore 2,3-dihydrobenzofurans(DHB) in comparison to selected some derivatives drugs by using molecular docking and molecular dynamics, as well as ADMET studies. The online database “Molinspiration online server” was used to detect the physicochemical pharmacokinetics and drug likeness score of DHB drugs. For estimation of molecular docking, six pathogens, such as Aspergillus niger (PDB id: 1kum), Candida albicans (3dra), Escherichia coli (6og7), Salmonella typhi (4k6l), Influenza (1ru7), and Hepatitis C (4tyd), were chosen due to close biological studies.
Results
From Molinspiration online server has showed that DHB did not violate the “Lipinski five rule” as drugs, leading compound for molecular docking exhibited the potential interaction to the active residue. The binding affinity of DHB2 (−7.00 kcal/mol) against 3dra was higher than DHB8 (−6.40 kcal/mol) and DHB (5.70 kcal/mol) for compounds. The results of molecular docking show that the compounds mentioned in this study are not equally effective against pathogens, such as fungi, viruses, and bacteria. However, DHB2, DHB3, and DHB 8 compounds can work against almost given pathogens which results are derived from auto dock vina in terms of binding affinity around 6.00 kcal/mol, and Fire Dock has values from about 38.0 to 42.0 kcal/mol. To explore the dynamic nature of the interaction, 50 ns molecular dynamics (MD) simulation was performed on the selected protein-DHB complexes. Thus, DHB 8 has greater potential to interact for further for fungi.
Conclusion
Finding from this study can play an effective role as a drug in any biological system. This study as well recommends to researchers to synthesize these DHBs for evaluation of its biological activity.
Graphical abstract
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Lawande PP, Sontakke VA, Kumbhar NM, Bhagwat TR, Ghosh S, Shinde VS. Polyhydroxylated azetidine iminosugars: Synthesis, glycosidase inhibitory activity and molecular docking studies. Bioorg Med Chem Lett 2017; 27:5291-5295. [PMID: 29074258 DOI: 10.1016/j.bmcl.2017.10.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 11/28/2022]
Abstract
An efficient and practical strategy for the synthesis of unknown azetidine iminosugars (2S,3R,4S)-2-((R)-1,2-dihydroxyethyl)-3-hydroxy-4-(hydroxymethyl)azetidine 2, (2S,3r,4R)-3-hydroxy-2,4-bis(hydroxymethyl)azetidine 3 and (2S,3R,4S)-3-hydroxy-4-(hydroxymethyl)-N-methylazetidine-2-carboxylic acid 4, starting from the d-glucose has been reported. The methodology involves preparation of the 3-amino-N-benzyloxycarbonyl-3-deoxy-6-O-tert-butyldimethylsillyl-1,2-O-isopropylidene-α-d-glucofuranose 9, which was converted to the C-5-OMs derivative 11. Intramolecular nucleophilic displacement of the C-5-OMs group with in situ generated 3-amino functionality provided the required key azetidine ring skeletons 10 with additional hydroxymethyl group. Removal of 1,2-acetonide protection, followed by reduction and hydrogenolysis afforded azetidine iminosugar 2. Alternatively, removal of 1,2-acetonide group and chopping of C1-anomeric carbon gave C2-aldehyde that on reduction or oxidation followed by hydrogenolysis gave 2,4-bis(hydroxymethyl) azetidine iminosugars 3 and N-methylazetidine-2-carboxylic acid 4 respectively. The glycosidase inhibitory activity of 2-4 iminosugars was screened against various glycosidase enzymes and compared with a standard miglitol. Amongst synthesized targets, the compound 2 was found to be more potent amyloglucosidase inhibitor than miglitol. These results were supported by molecular docking studies.
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Affiliation(s)
- Pravin P Lawande
- Department of Chemistry, Savitribai Phule Pune University (Formerly, University of Pune), Pune 411007, India
| | - Vyankat A Sontakke
- Department of Chemistry, Savitribai Phule Pune University (Formerly, University of Pune), Pune 411007, India
| | - Navanath M Kumbhar
- Department of Chemistry, Savitribai Phule Pune University (Formerly, University of Pune), Pune 411007, India
| | - Tanay R Bhagwat
- Department of Microbiology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India
| | - Sougata Ghosh
- Department of Microbiology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune 411016, India
| | - Vaishali S Shinde
- Department of Chemistry, Savitribai Phule Pune University (Formerly, University of Pune), Pune 411007, India.
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Pierra Rouvière C, Amador A, Badaroux E, Convard T, Da Costa D, Dukhan D, Griffe L, Griffon JF, LaColla M, Leroy F, Liuzzi M, Loi AG, McCarville J, Mascia V, Milhau J, Onidi L, Paparin JL, Rahali R, Sais E, Seifer M, Surleraux D, Standring D, Dousson C. Synthesis of potent and broad genotypically active NS5B HCV non-nucleoside inhibitors binding to the thumb domain allosteric site 2 of the viral polymerase. Bioorg Med Chem Lett 2016; 26:4536-4541. [PMID: 27520942 DOI: 10.1016/j.bmcl.2016.01.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 12/21/2022]
Abstract
The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for selective inhibition. This Letter describes the discovery of a new family of HCV NS5B non-nucleoside inhibitors, based on the bioisosterism between amide and phosphonamidate functions. As part of this program, SAR in this new series led to the identification of IDX17119, a potent non-nucleoside inhibitor, active on the genotypes 1b, 2a, 3a and 4a. The structure and binding domain of IDX17119 were confirmed by X-ray co-crystallization study.
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Affiliation(s)
- Claire Pierra Rouvière
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France.
| | - Agnès Amador
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Eric Badaroux
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Thierry Convard
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Daniel Da Costa
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - David Dukhan
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Ludovic Griffe
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Jean-François Griffon
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Massimiliano LaColla
- Idenix Employee of the Former Idenix Pharmaceuticals Company, One Kendall Square, Ste B14104, Cambridge, MA 02139-1573, USA
| | - Frédéric Leroy
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Michel Liuzzi
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Laboratorio Cooperativo Idenix-Università di Cagliari, Zona Industriale di Macchiareddu, Sesta strada ovest, 09010 Uta (Cagliari), Italy
| | - Anna Giulia Loi
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Laboratorio Cooperativo Idenix-Università di Cagliari, Zona Industriale di Macchiareddu, Sesta strada ovest, 09010 Uta (Cagliari), Italy
| | - Joe McCarville
- Idenix Employee of the Former Idenix Pharmaceuticals Company, One Kendall Square, Ste B14104, Cambridge, MA 02139-1573, USA
| | - Valeria Mascia
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Laboratorio Cooperativo Idenix-Università di Cagliari, Zona Industriale di Macchiareddu, Sesta strada ovest, 09010 Uta (Cagliari), Italy
| | - Julien Milhau
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Loredana Onidi
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Laboratorio Cooperativo Idenix-Università di Cagliari, Zona Industriale di Macchiareddu, Sesta strada ovest, 09010 Uta (Cagliari), Italy
| | - Jean-Laurent Paparin
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Rachid Rahali
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - Efisio Sais
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Laboratorio Cooperativo Idenix-Università di Cagliari, Zona Industriale di Macchiareddu, Sesta strada ovest, 09010 Uta (Cagliari), Italy
| | - Maria Seifer
- Idenix Employee of the Former Idenix Pharmaceuticals Company, One Kendall Square, Ste B14104, Cambridge, MA 02139-1573, USA
| | - Dominique Surleraux
- Idenix Employee of the Former Idenix Pharmaceuticals Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
| | - David Standring
- Idenix Employee of the Former Idenix Pharmaceuticals Company, One Kendall Square, Ste B14104, Cambridge, MA 02139-1573, USA
| | - Cyril Dousson
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP 50001, 34189 Montpellier Cedex 4, France
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7
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Parsy CC, Alexandre FR, Bidau V, Bonnaterre F, Brandt G, Caillet C, Cappelle S, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos LB, Leroy F, Liuzzi M, Loi AG, Moulat L, Chiara M, Rahali H, Roques V, Rosinovsky E, Savin S, Seifer M, Standring D, Surleraux D. Discovery and structural diversity of the hepatitis C virus NS3/4A serine protease inhibitor series leading to clinical candidate IDX320. Bioorg Med Chem Lett 2015; 25:5427-36. [DOI: 10.1016/j.bmcl.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
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8
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Alexandre FR, Brandt G, Caillet C, Chaves D, Convard T, Derock M, Gloux D, Griffon Y, Lallos L, Leroy F, Liuzzi M, Loi AG, Moulat L, Musiu C, Parsy C, Rahali H, Roques V, Seifer M, Standring D, Surleraux D. Synthesis and antiviral evaluation of a novel series of homoserine-based inhibitors of the hepatitis C virus NS3/4A serine protease. Bioorg Med Chem Lett 2015; 25:3984-91. [DOI: 10.1016/j.bmcl.2015.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 01/01/2023]
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Liu Z, Jenkinson SF, Vermaas T, Adachi I, Wormald MR, Hata Y, Kurashima Y, Kaji A, Yu CY, Kato A, Fleet GWJ. 3-Fluoroazetidinecarboxylic Acids and trans,trans-3,4-Difluoroproline as Peptide Scaffolds: Inhibition of Pancreatic Cancer Cell Growth by a Fluoroazetidine Iminosugar. J Org Chem 2015; 80:4244-58. [DOI: 10.1021/acs.joc.5b00463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zilei Liu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Sarah F. Jenkinson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Tom Vermaas
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Isao Adachi
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - Mark R. Wormald
- Glycobiology
Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Yukako Hata
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Yukiko Kurashima
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Akira Kaji
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Chu-Yi Yu
- CAS
Key Laboratory of Molecular Recognition and Function, Institute of
Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Atsushi Kato
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - George W. J. Fleet
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P.R. China
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