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Gopi B, Vijayakumar V. An efficient and simple approach for synthesizing indazole compounds using palladium-catalyzed Suzuki-Miyaura cross-coupling. RSC Adv 2024; 14:26494-26504. [PMID: 39175677 PMCID: PMC11339776 DOI: 10.1039/d4ra04633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024] Open
Abstract
A series of indazole derivatives (6a-6i and 7a-7i) has been synthesized using Suzuki Miyaura cross-coupling with a palladium catalyst from readily available starting materials. An efficient and reliable methodology was employed for the synthesis, and the compounds were thoroughly characterized using 1H NMR, 13C NMR, FT-IR, and HRMS analysis to confirm their structural integrity and purity. Density function theory (DFT) computation identified four compounds (6g, 6h, 7g, and 7h) with significant energy band gaps. Additionally, the molecular electrostatic potential study highlighted the distinct electrical characteristics of these indazole molecules. Subsequent molecular docking investigations were carried out using the AUTODOCK method with two separate protein data bank (PDB) structures (6FEW, 4WA9) involved in renal cancer pathways. The results showed that eight substances PDB: 6FEW (6g, 6h, 7g, and 7h) and PDB: 4WA9 (6a, 6c, and 7c, 7g) had the highest binding energies, indicating their potential as therapeutic agents for treating kidney cancer.
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Affiliation(s)
- Bandaru Gopi
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore 632014 India
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Gopi B, Vijayakumar V. Synthesis molecular docking and DFT studies on novel indazole derivatives. RSC Adv 2024; 14:13218-13226. [PMID: 38655475 PMCID: PMC11037238 DOI: 10.1039/d4ra02151g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
The amide bond is an important functional group used in various fields of chemistry, including organic synthesis, drug discovery, polymers, and biology. Although normal amides are planar, and the amide has an N-C(O) bond, herein, the 26 indazole derivatives were reported via amide cross-coupling (8a-8z). Using IR, 1H NMR, 13C NMR, and mass spectrometry, all of the produced compounds were analysed. A DFT computational study was also conducted using GAUSSIAN 09-Gaussian View 6.1, which revealed that 8a, 8c, and 8s had the most substantial HOMO-LUMO energy gap. The effectiveness of indazole moieties with renal cancer-related protein (PDB: 6FEW) was assessed by docking the derivatives using Autodock 4. The analysis showed that derivatives 8v, 8w, and 8y had the highest binding energies.
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Affiliation(s)
- Bandaru Gopi
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore - 632014 India
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Santiago-Silva KMD, Camargo P, Felix da Silva Gomes G, Sotero AP, Orsato A, Perez CC, Nakazato G, da Silva Lima CH, Bispo M. In silico approach identified benzoylguanidines as SARS-CoV-2 main protease (M pro) potential inhibitors. J Biomol Struct Dyn 2023; 41:7686-7699. [PMID: 36124832 DOI: 10.1080/07391102.2022.2123396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
The coronavirus disease-2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), became the highest public health crisis nowadays. Although the use of approved vaccines for emergency immunization and the reuse of FDA-approved drugs remains at the forefront, the search for new, more selective, and potent drug candidates from synthetic compounds is also a viable alternative to combat this viral disease. In this context, the present study employed a computational virtual screening approach based on molecular docking and molecular dynamics (MD) simulation to identify possible inhibitors for SARS-CoV-2 Mpro (main protease), an important molecular target required for the maturation of the various polyproteins involved in viral replication. The virtual screening approach selected four potential inhibitors against SARS-CoV-2 Mpro. In addition, MD simulation studies revealed changes in the positions of the ligands during the simulations compared to the complex obtained in the molecular docking studies, showing the benzoylguanidines LMed-110 and LMed-136 have a higher affinity for the active site compared to the other structures that tended to leave the active site. Besides, there was a better understanding of the formation and stability of the existing H-bonds in the formed complexes and the energetic contributions to the stability of the target-ligand molecular complexes. Finally, the in silico prediction of the ADME profile suggested that LMed-136 has drug-like characteristics and good pharmacokinetic properties. Therefore, from the present study, it can be suggested that these structures can inhibit SARS-CoV-2 Mpro. Nevertheless, further studies are needed in vitro assays to investigate the antiviral properties of these structures against SARS-CoV-2.
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Affiliation(s)
- Kaio Maciel de Santiago-Silva
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Priscila Camargo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Gabriel Felix da Silva Gomes
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Ana Paula Sotero
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Orsato
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Carla Cristina Perez
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Gerson Nakazato
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Camilo Henrique da Silva Lima
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelle Bispo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
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Kumari M, Dasgupta S, Panda S, Bera SK, Datta A, Lahiri GK. Unique Metal-Ligand Interplay in Directing Discrete and Polymeric Derivatives of Isomeric Azole-Carboxylate. Varying Electronic Form, C-C Coupling, and Receptor Feature. Inorg Chem 2023; 62:7779-7794. [PMID: 37163348 DOI: 10.1021/acs.inorgchem.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This article dealt with the ruthenium and osmium derivatives of isomeric 1H-indazole-3-carboxylic acid/2H-indazole-3-carboxylic acid (H2L1) and 1H-benzimidazole-2-carboxylic acid (H2L2) along with the π-acidic bpy (bpy = 2,2'-bipyridine) and pap (pap = 2-phenylazopyridine) co-ligands. It thus extended structurally authenticated monomeric ([(bpy)2RuII(HL1-)]ClO4 [1]ClO4, (pap)2RuII(L12-) 2, (bpy)2OsII(L12-) 3, (pap)2OsII(L12-) 4, (bpy)2RuII(L22-) 5, (bpy)2OsII(L22-) 8, and (pap)2OsII(L22-) 9) and dimeric ([(bpy)2RuII(μ-L22-)RuII(bpy)2](ClO4)2 [6](ClO4)2) complexes. It also described modified L2'2- (L2'2- = 2,2'-bisbenzimidazolate)-bridged [(pap)2RuII(μ-L2'2-)RuII(pap)2](ClO4)2 [7](ClO4)2, where L2'2- was developed selectively with the {Ru(pap)2} metal fragment via in situ intermolecular C-C coupling of the two units of decarboxylated benzimidazolate. Moreover, chemical oxidation (OsII to OsIII) of (bpy)2OsII(L12-) 3 (E0 = 0.11 V versus SCE) and (bpy)2OsII(L22-) 8 (E0 = 0.12 V versus SCE) by AgClO4 yielded unprecedented OsIII-AgI derived polymeric {[(bpy)2OsIII-L12--AgI(CH3CN)](ClO4)2}n {[10](ClO4)2}n and dimeric [(bpy)2OsIII-L22--AgI(CH3CN)](ClO4)2 [11](ClO4)2 complexes as a function of trans and cis orientations of the active N2 donor with special reference to the carboxylate O2 of L2-, respectively. Microscopic (FE-SEM, TEM-EDX, and AFM) and DLS experiments suggested a homogeneously dispersed hollow spherical shaped morphology of {[10](ClO4)2}n with an average particle size of 200-400 nm as well as its non-dissociative feature in the aprotic medium. Experimental (structure, spectroscopy, and electrochemistry) and theoretical (DFT/TD-DFT) explorations revealed a redox non-innocent feature of L2- in the present coordination situations and the selective anion sensing (X = F-, CN-, and OAc-) event of [1]ClO4 involving a free NH group at the backface of HL1-, which proceeded via the NH···X hydrogen bonding interaction.
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Affiliation(s)
- Maya Kumari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Souradip Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjib Panda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sudip Kumar Bera
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Goutam Kumar Lahiri
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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