<i>In vitro</i>and computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M<sup>Pro</sup>inhibitors

Aljuhani, Ateyatallah; Ahmed, Hany E. A.; Ihmaid, Saleh; Omar, Abdelsattar M.; Thagfan, Sultan S. Al; Alahmadi, Yaser M.; Ahmad, Iqrar; Patel, Harun; Ahmed, Sahar; Almikhlafi, Mohannad A.; El‐Agrody, Ahmed M.; Zayed, Mohamed F.; Turkistani, Safaa A.; Abulkhair, Shorouk H.; Almaghrabi, Mohammed; Salama, Samir A.; Al‐Karmalawy, Ahmed A.; Abulkhair, Hamada S.

doi:10.1039/d2ra04015h

Cited by 40 publications

(18 citation statements)

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“…Both covalent and van der Waals interactions were described by OPLS-AA force field [ 50 , 51 ], with the exception for the atoms of the imine group (-C=N-), explicit parametrization of which was introduced in OPLS_2005 force field [ 52 ] and is essential for accurate description of salphen compounds. While many improvements were introduced over the years with more recent parametrizations [ 53 , 54 , 55 , 56 ], such as more precise torsions for DNA backbone chain and better description of nucleic acid interaction, the OPLS-AA force field is still widely used for molecular simulations in liquid state, such as including recent studies of SARS-CoV-2 inhibitors [ 57 ], chromophores [ 58 ] and electrolytes for novel batteries [ 59 ]. It is also implemented in many open source toolkits for building input files for molecular dynamics simulations, such as Moltemplate [ 60 ], used in this work.…”

Section: Methodsmentioning

confidence: 99%

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

et al. 2022

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Manipulation of nanoscale objects using molecular self-assembly is a potent tool to achieve large scale nanopatterning with small effort. Coordination polymers of bis-salphen compounds based on zinc have demonstrated their ability to align carbon nanotubes into micro-scale networks with an unusual “rings-and-rods” pattern. This paper investigates how the compounds interact with pristine and functionalized graphene using density functional theory calculations and molecular dynamic simulations. Using the free energy perturbation method we will show how the addition of phenyl side groups to the core compound and functionalization of graphene affect the stability, mobility and conformation adopted by a dimer of bis-(Zn)salphen compound adsorbed on graphene surface and what it can reveal about the arrangement of chains of bis-(Zn)salphen polymer around carbon nanotubes during the self-assembly of microscale networks.

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Section: Methodsmentioning

confidence: 99%

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

et al. 2022

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“…The discrepancy between the backbones of a protein from its initial structural conformation to its final positioning is measured using RMSD. [32,39,40] The variations obtained during the simulation could be used to estimate the protein's stability compared with its conformation. The fewer variances there are, the more stable the protein structure.…”

Section: Simulation Studymentioning

confidence: 99%

Benzimidazole and piperidine containing novel 1,2,3‐triazole hybrids as anti‐infective agents: Design, synthesis, in silico and in vitro antimicrobial efficacy

Mendapara,

Vaghasiya,

Rajani

et al. 2023

J Biochem & Molecular Tox

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Cu alkyne‐azide cycloaddition was used to easily synthesize a library of novel heterocycles containing benzimidazole and piperidine based 1,2,3‐triazole(7a–7l) derivatives. The synthesized analogs were characterized by various spectroscopic techniques like FTIR, 1H nuclear magnetic resonance (NMR), 13C NMR, and mass spectrometry. All these novel bioactive compounds (7a–7l) were evaluated for in vitro antibacterial and antifungal efficacy. Compound 7k exhibited appreciable potent activity against Escherichia coli strain. Compounds 7a, 7b, 7f, and 7i showed excellent potent activity against all bacterial strains. Compound 7b, 7c, 7d, and 7g derivatives showed excellent effects when tested in vitro for antifungal activity against various fungal strains. Additionally, a molecular docking investigation revealed that compound 7k has the ability to bind to the active site of the E. coli DNA gyrase subunit protein and form hydrogen bonds with significant amino acid residues Asp73 and Asp49 in the active sites. In a 100 ns molecular dynamics simulation, the E. coli DNA gyrase protein's steady capacity to bind compound 7k was shown by the low measured root mean square deviation, which was an indication of the complex's conformational stability.

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“…The docking process specifications were applied as described earlier. [90][91][92][93] The best pose for each studied compound was selected based on the score, binding mode compared to the co-crystallized inhibitor, and RMSD value as well. [94][95][96]…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

Design and synthesis of novel quinazolinone–chalcone hybrids as potential apoptotic candidates targeting caspase-3 and PARP-1:in vitro, molecular docking, and SAR studies

et al. 2022

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In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M^Proinhibitors

Abstract: An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro).

Cited by 40 publications

References 75 publications

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

Benzimidazole and piperidine containing novel 1,2,3‐triazole hybrids as anti‐infective agents: Design, synthesis, in silico and in vitro antimicrobial efficacy

Design and synthesis of novel quinazolinone–chalcone hybrids as potential apoptotic candidates targeting caspase-3 and PARP-1:in vitro, molecular docking, and SAR studies

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In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-MProinhibitors

Abstract: An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro).

Cited by 40 publications

References 75 publications

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study

Benzimidazole and piperidine containing novel 1,2,3‐triazole hybrids as anti‐infective agents: Design, synthesis, in silico and in vitro antimicrobial efficacy

Design and synthesis of novel quinazolinone–chalcone hybrids as potential apoptotic candidates targeting caspase-3 and PARP-1:in vitro, molecular docking, and SAR studies

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In vitroand computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M^Proinhibitors