Screening and Identification of Natural Product‐Like Compounds as Potential Antibacterial Agents Targeting FemC of <i>Staphylococcus aureus</i>: An in‐Silico Approach

Dalal, Vikram; Kumari, Reena

doi:10.1002/slct.202201728

Cited by 30 publications

(5 citation statements)

References 70 publications

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“…The Ramachandran plot of Rv1250 generated by PROCHECK showed that 89.9% of the amino acid residues are in the most favoured region, 9.4% in the additional allowed region, 0.6% in the generously allowed region and 0.1% in disallowed region as shown in Figure 2 . The results showed that no residues were in the outliners region and similar scores were stated by Dhankhar et al (2020) , Dalal and Kumari (2022) .…”

Section: Resultssupporting

confidence: 79%

Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis

et al. 2023

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Computational prediction and protein structure modeling have come to the aid of various biological problems in determining the structure of proteins. These technologies have revolutionized the biological world of research, allowing scientists and researchers to gain insights into their biological questions and design experimental research much more efficiently. Pathogenic Mycobacterium spp. is known to stay alive within the macrophages of its host. Mycobacterium tuberculosis is an acid-fast bacterium that is the most common cause of tuberculosis and is considered to be the main cause of resistance of tuberculosis as a leading health issue. The genome of Mycobacterium tuberculosis contains more than 4,000 genes, of which the majority are of unknown function. An attempt has been made to computationally model and dock one of its proteins, Rv1250 (MTV006.22), which is considered as an apparent drug-transporter, integral membrane protein, and member of major facilitator superfamily (MFS). The most widely used techniques, i.e., homology modeling, molecular docking, and molecular dynamics (MD) simulation in the field of structural bioinformatics, have been used in the present work to study the behavior of Rv1250 protein from M. tuberculosis. The structure of unknown TB protein, i.e., Rv1250 was retrived using homology modeling with the help of I-TASSER server. Further, one of the sites responsible for infection was identified and docking was done by using the specific Isoniazid ligand which is an inhibitor of this protein. Finally, the stability of protein model and analysis of stable and static interaction between protein and ligand molecular dynamic simulation was performed at 100 ns The designing of novel Rv1250 enzyme inhibitors is likely achievable with the use of proposed predicted model, which could be helpful in preventing the pathogenesis caused by M. tuberculosis. Finally, the MD simulation was done to evaluate the stability of the ligand for the specific protein.

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Section: Resultssupporting

confidence: 79%

Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis

et al. 2023

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“…Overall, the fluctuation intensity remains below 2.0 Å except for some residues representing a loop in the enzyme (Figure 6(C and D)). All complexes had low RMSF Coulomb (electrostatic potential), and Lennard Jones (Pauli repulsion, and Hydrophobic/Van Der Waals attractions) [31] …”

Section: Resultsmentioning

confidence: 99%

“…All complexes had low RMSF Coulomb (electrostatic potential), and Lennard Jones (Pauli repulsion, and Hydrophobic/Van Der Waals attractions). [31]…”

Section: Root Mean Square Fluctuations (Rmsf)mentioning

confidence: 99%

Computational and Retrosynthetic Investigation of Isoxazole‐Bearing Chalcones as Antioxidant Activate Compounds

Moukhliss

Koubi

Alaqarbeh³

et al. 2023

ChemistrySelect

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Peroxiredoxin 5 (1HD2) is an antioxidant enzyme that catalyzes the decrease of peroxide, and act as a regulator of Redox signaling. It is a potential target for working on new antioxidants. 3D-QSAR method was applied to a set of isoxazoles by using the comparative analysis of molecular fields (CoMFA and CoMSIA). Five new drug candidates (Pr1-Pr5) have been proposed. The study of the interactions between the drug candidate and antioxidant receptor 1HD2 was done by molecular docking. The results of the ADME (Absorption, Distribution, Metabolism, and Excretion) showed that these drug candidates are orally bioavailable and have high gastrointestinal absorption and good permeability. Molecular dynamics was used at 100 ns to study the stability of the MA-1HD2 and Pr5-1HD2 complexes obtained after molecular docking. Using the retrosynthesis approach, we have proposed a pathway for synthesizing the drug candidates. This study provides useful information on the antioxidant activity of isoxazolebased compounds.

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“…Then, hydrogens were added; average charges were assigned using Kollman charges, and torsional degrees of freedom were detected using AutoDockTools (ADT). The docking grid was defined to include active site residues , D22, H72, and H143. The x , y , and z coordinates of the center of the docking grid were set to −1.867, 6.077, and 37.778, respectively.…”

Section: Methodsmentioning

confidence: 99%

Structural Insights into the Catalytic Activity of Cyclobacterium marinum N-Acetylglucosamine Deacetylase

Hu,

Xu,

Xie

et al. 2023

J. Agric. Food Chem.

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N-Acetylglucosamine deacetylase from Cyclobacterium marinum (CmCBDA) is a highly effective and selective biocatalyst for the production of D-glucosamine (GlcN) from N-acetylglucosamine (GlcNAc). However, the underlying catalytic mechanism remains elusive. Here, we show that CmCBDA is a metalloenzyme with a preference for Ni 2+ over Mn 2+ . Crystal structures of CmCBDA in complex with Ni 2+ and Mn 2+ revealed slight remodeling of the CmCBDA active site by the metal ions. We also demonstrate that CmCBDA exists as a mixture of homodimers and monomers in solution, and dimerization is indispensable for catalytic activity. A mutagenesis analysis also indicated that the active site residues Asp22, His72, and His143 as well as the residues involved in dimerization, Pro52, Trp53, and Tyr55, are essential for catalytic activity. Furthermore, a mutation on the protein surface, Lys219Glu, resulted in a 2.3-fold improvement in the deacetylation activity toward GlcNAc. Mechanistic insights obtained here may facilitate the development of CmCBDA variants with higher activities.

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Screening and Identification of Natural Product‐Like Compounds as Potential Antibacterial Agents Targeting FemC of Staphylococcus aureus: An in‐Silico Approach

Cited by 30 publications

References 70 publications

Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis

Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis

Computational and Retrosynthetic Investigation of Isoxazole‐Bearing Chalcones as Antioxidant Activate Compounds

Structural Insights into the Catalytic Activity of Cyclobacterium marinum N-Acetylglucosamine Deacetylase

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