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Bhat MA, Jan M, Manzoor U, Shalla AH, Butcher RJ, Jasinski JP. Synthesis of novel 2,5-bis(substituted thio)-1,3,4-thiadiazoles by acid catalyzed intermolecular cyclization reactions of substituted dithiocarbazates as a possible 2019-nCoV main protease inhibitor. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Chopra A, Fatima A, Srivastava SK, Siddiqui N, Javed S. N-[4-(phenyl telluro) butyl] phthalimide: Synthesis, spectral characterization, DFT studies and its complexes with mercury salts. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Martín-Encinas E, Rubiales G, Knudsen BR, Palacios F, Alonso C. Fused chromeno and quinolino[1,8]naphthyridines: Synthesis and biological evaluation as topoisomerase I inhibitors and antiproliferative agents. Bioorg Med Chem 2021; 40:116177. [PMID: 33962152 DOI: 10.1016/j.bmc.2021.116177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 01/18/2023]
Abstract
The synthesis of 1,8-naphthyridine derivatives fused with other heterocycles, such as chromenes and quinolines, as well as their behaviour as topoisomerase I inhibitors is studied. The preparation is carried out through a direct and simple process as an intramolecular [4 + 2] cycloaddition reaction between functionalized aldimines, obtained by the condensation of 2-aminopyridine and unsaturated aldehydes, and olefins. In particular, while no clear inhibitory activity is observed for chromeno[4,3-b][1,8]naphthyridine fused heterocycles, a very different result is observed for quinolino[4,3-b][1,8]naphthyridine derivatives. Experimental assays indicated that quinolino[4,3-b][1,8]naphthyridines inhibited the topoisomerase I enzymatic reaction behaving like a poison, as occurs with the natural TopI inhibitor, camptothecin. Furthermore, the cytotoxic effect on cell lines derived from human lung adenocarcinoma (A549), human ovarian carcinoma (SKOV3), and on non-cancerous lung fibroblasts cell line (MRC5) was also screened.
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Affiliation(s)
- Endika Martín-Encinas
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
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Novel monoanionic diphenate-nicotinamide/N,N-diethylnicotinamide complexes of NiII, ZnII. Synthesis, structural investigations and hydrogen adsorption study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Synthesis of novel hybrid quinolino[4,3-b][1,5]naphthyridines and quinolino[4,3-b][1,5]naphthyridin-6(5H)-one derivatives and biological evaluation as topoisomerase I inhibitors and antiproliferatives. Eur J Med Chem 2020; 195:112292. [DOI: 10.1016/j.ejmech.2020.112292] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/28/2020] [Accepted: 03/28/2020] [Indexed: 12/18/2022]
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Martín-Encinas E, Conejo-Rodríguez V, Miguel JA, Martínez-Ilarduya JM, Rubiales G, Knudsen BR, Palacios F, Alonso C. Novel phosphine sulphide gold(i) complexes: topoisomerase I inhibitors and antiproliferative agents. Dalton Trans 2020; 49:7852-7861. [DOI: 10.1039/d0dt01467b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gold(i) increases the cytotoxicity of phosphine sulfide quinolines against cancer cell lines, while heterocycles maintain the TopI inhibitory activity.
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Affiliation(s)
- Endika Martín-Encinas
- Department of Organic Chemistry I
- Faculty of Pharmacy
- University of Basque Country (UPV/EHU)
- Vitoria-Gasteiz
- Spain
| | | | - Jesús A. Miguel
- IU CINQUIMA/Química Inorgánica
- Faculty of Science
- University of Valladolid
- Valladolid
- Spain
| | | | - Gloria Rubiales
- Department of Organic Chemistry I
- Faculty of Pharmacy
- University of Basque Country (UPV/EHU)
- Vitoria-Gasteiz
- Spain
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO)
- University of Aarhus
- Aarhus
- Denmark
| | - Francisco Palacios
- Department of Organic Chemistry I
- Faculty of Pharmacy
- University of Basque Country (UPV/EHU)
- Vitoria-Gasteiz
- Spain
| | - Concepción Alonso
- Department of Organic Chemistry I
- Faculty of Pharmacy
- University of Basque Country (UPV/EHU)
- Vitoria-Gasteiz
- Spain
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Martín-Encinas E, Rubiales G, Knudssen BR, Palacios F, Alonso C. Straightforward synthesis and biological evaluation as topoisomerase I inhibitors and antiproliferative agents of hybrid Chromeno[4,3-b][1,5]Naphthyridines and Chromeno[4,3-b][1,5]Naphthyridin-6-ones. Eur J Med Chem 2019; 178:752-766. [DOI: 10.1016/j.ejmech.2019.06.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
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Bhat MA, Jameel S, Jan M, Rather MA, Bhat SA, Butcher RJ, Srivastava SK. Synthesis, characterization, computational and cytotoxic evaluation of novel [N, N-dialkyl ammonium] [diphenyl/ethyl phosphoryl oxides]. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Synthesis, characterization, and theoretical studies of (E)-t-butyl-2-((E)-2-methyl-3-phenylallylidene) hydrazine carboxylate and (E)-t-butyl-2-((E)-3-phenylallylidene) hydrazine carboxylates as a possible Mcl-1 antagonists. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Synthesis, crystal structure, DFT study, in vitro and in silico molecular docking of novel bis (aroyl selenourea) derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Bhat MA, Lone SH, Agim J, Butcher RJ, Srivastava SK. Synthesis, spectral characterization, crystallographic analysis, DFT studies, bioevaluation and anion exchange reactions of 1-(3-chlorophenyl)-4-(3-phenylseleno propyl) piperazinium chloride. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Bhat MA, Lone SH, Ali S, Srivastava SK. Synthesis, spectral characterization, reactivity and DFT studies of novel ligand phenylseleno benzylacetate (L) and its complexes with group 12 metal chlorides. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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14
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Tejería A, Pérez-Pertejo Y, Reguera RM, Carbajo-Andrés R, Balaña-Fouce R, Alonso C, Martin-Encinas E, Selas A, Rubiales G, Palacios F. Antileishmanial activity of new hybrid tetrahydroquinoline and quinoline derivatives with phosphorus substituents. Eur J Med Chem 2018; 162:18-31. [PMID: 30408746 DOI: 10.1016/j.ejmech.2018.10.065] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022]
Abstract
Heterocyclic compounds, such as hybrid tetrahydroquinoline and quinoline derivatives with phosphorated groups, have been prepared by multicomponent cycloaddition reaction between phosphorus-substituted anilines, aldehydes and styrenes. The antileishmanial activity of these compounds has been evaluated on both promastigotes and intramacrophagic amastigotes of Leishmania infantum. Good antileishmanial activity of functionalized tetrahydroquinolines 4a, 5a, 6b and quinoline 8b has been observed with similar activity than the standard drug amphotericin B and close selective index (SI between 43 and 57) towards L. infantum amastigotes to amphotericin B. Special interest shows tetrahydroquinolylphosphine sulfide 5a with an EC50 value (0.61 ± 0.18 μM) similar to the standard drug amphotericin B (0.32 ± 0.05 μM) and selective index (SI = 56.87). In addition, compound 4c shows remarkable inhibition on Leishmania topoisomerase IB. Parallel theoretical study of stereoelectronic properties, application of docking-based virtual screening methods, along with molecular electrostatic potential and predictive druggability analyses are also reported.
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Affiliation(s)
- Ana Tejería
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Rubén Carbajo-Andrés
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Endika Martin-Encinas
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Asier Selas
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain.
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Bhat MA, Lone SH, Srivastava SK. 1-(3-Chlorophenyl)-4-(3-phenylseleno propyl) piperazine (L); synthesis, spectroscopic characterization, DFT studies, antimicrobial evaluation and its reactivity toward group 12 metal chlorides. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1489126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Muzzaffar A. Bhat
- School of Studies in Chemistry, Jiwaji University, Gwalior, India
- Department of Chemistry, Islamic University of Science and Technology, Awantipora, Kashmir, India
| | - Shabir H. Lone
- Department of Chemistry, Govt Degree College Anantnag, Kashmir, India
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Bhat MA, Lone SH, Butcher RJ, Srivastava SK. Theoretical and experimental investigations into structural, electronic, molecular and biological properties of 4-(3-chlorophenyl)-1-(3-chloropropyl) piperazin-1-ium chloride. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Bhat MA, Lone SH, Srivastava SK. Synthesis, spectroscopic characterization, DFT studies and biological activity of bis (1-(ethyl) piperidine) diselenide (L) and its complexes with selected group 12 metal halides. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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