Physicochemical stability study of protein–benzoic acid complexes using molecular dynamics simulations

Arooj, Mahreen; Shehadi, Ihsan A.; Nassab, Chahlaa; Mohamed, Ahmed A.

doi:10.1007/s00726-020-02897-2

Cited by 20 publications

(16 citation statements)

References 41 publications

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“…For S protein, the RMSD (based on the analysis of Cα) of D614G(0.4894485) and D614G&A222V (0.5085670) has a certain decline compared with wild type (0.5376845), this suggests that the mutation of the residue located on No. 614 to glycine(G) from aspartic acid (D) promoted S protein stability (Arooj et al, 2020), the stability of the ascension is proportional to the effectiveness (Zhang et al, 2020). This is also consistent with current epidemiological data.…”

Section: Discussionmentioning

confidence: 99%

“…During the stable period (the latter 50ns) of the simulation process, the two proteins and their mutants showed different properties. For S protein, the RMSD (based on the analysis of Cα) of D614G, D614G&A222V, and penta-site mutant has a certain decline compared with wild type, this suggests that the D614G mutation promoted S protein stability 37 , the promotion of the stability is proportional to the decline degree 18 . This is also consistent with current epidemiological data.…”

Section: Discussionmentioning

confidence: 99%

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Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2

Lon

Xi²,

Zhong³

et al. 2021

Preprint

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SARS-CoV-2 has been spreading rapidly since 2019 and has produced large-scale mutations in the genomes. Differences in gene sequences may lead to changes in protein structure and traits, which would have a great impact on the epidemiological characteristics. In this study, we selected the key mutations of SARS-CoV-2, including D614G and A222V of S protein and Q57H of ORF3a protein, to conduct molecular dynamics simulation and analysis on the structures of the mutant proteins. The results suggested that D614G improved the stability of S protein, while A222V enhanced the ability of protein to react with the outside environment. Q57H enhanced the structural flexibility of ORF3a protein. Our findings could complete the mechanistic link between genotype--phenotype--epidemiological characteristics in the study of SARS-CoV-2. We also found no significant changes in the antigenicity of S protein, ORF3a protein and their mutants, which provides reference for vaccine development and application.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2

Lon

Xi²,

Zhong³

et al. 2021

Preprint

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“…Furthermore, the RMSF values for M pro /GSRY complex were calculated ( Arooj, Shehadi, Nassab, & Mohamed, 2020 ). As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification of lactoferrin-derived peptides as potential inhibitors against the main protease of SARS-CoV-2

Zhao

et al. 2022

LWT

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COVID-19 is a global health emergency that causes serious concerns. A global effort is underway to identify drugs for the treatment of COVID-19. One possible solution to the present problem is to develop drugs that can inhibit SARS-CoV-2 main protease (M pro ), a coronavirus protein that been considered as one among many drug targets. In this work, lactoferrin from Bos taurus L. was in silico hydrolyzed. The bioactivity, water solubility, and ADMET properties of the generated peptides were predicted using various online tools. The molecular interactions between M pro and the peptides were studied using molecular docking and molecular dynamic simulation. The results demonstrated that peptide GSRY was predicted to have better physicochemical properties, and the value of ‘-C DOCKER interaction energy’ between peptide GSRY and M pro was 80.8505 kcal/mol. The interaction between the peptide GSRY and the native ligand N3 co-crystallized with M pro had overlapped amino acids, i.e., HIS163, GlY143, GLU166, GLN189 and MET165. Molecular dynamic simulation revealed that M pro /GSRY complexes were stable. Collectively, the peptide GSRY may be a potential candidate drug against M pro of SARS-CoV-2.

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“…Molecular dynamics (MD) simulations are extensively used to explore the stability and binding of various protein ligand complexes [28][29][30]. In order to elucidate the stability of complex structures, both proteins were bound with best binding compound 3 and subjected to MD simulations.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Solvent-Free Synthesis, In Vitro and In Silico Studies of Novel Potential 1,3,4-Thiadiazole-Based Molecules against Microbial Pathogens

et al. 2022

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A new series of 1,3,4-thiadiazoles was synthesized by the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate (2) with selected derivatives of hydrazonoyl halide by grinding method at room temperature. The chemical structures of the newly synthesized derivatives were resolved from correct spectral and microanalytical data. Moreover, all synthesized compounds were screened for their antimicrobial activities using Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Bacillus subtilis, Staphylococcus aureus, and Candida albicans. However, compounds 3 and 5 showed significant antimicrobial activity against all tested microorganisms. The other prepared compounds exhibited either only antimicrobial activity against Gram-positive bacteria like compounds 4 and 6, or only antifungal activity like compound 7. A molecular docking study of the compounds was performed against two important microbial enzymes: tyrosyl-tRNA synthetase (TyrRS ) and N-myristoyl transferase (Nmt). The tested compounds showed variety in binding poses and interactions. However, compound 3 showed the best interactions in terms of number of hydrogen bonds, and the lowest affinity binding energy (–8.4 and –9.1 kcal/mol, respectively). From the in vitro and in silico studies, compound 3 is a good candidate for the next steps of the drug development process as an antimicrobial drug.

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Physicochemical stability study of protein–benzoic acid complexes using molecular dynamics simulations

Cited by 20 publications

References 41 publications

Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2

Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2

Identification of lactoferrin-derived peptides as potential inhibitors against the main protease of SARS-CoV-2

Solvent-Free Synthesis, In Vitro and In Silico Studies of Novel Potential 1,3,4-Thiadiazole-Based Molecules against Microbial Pathogens

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