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Figure 14 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021

Figure 14 Protein interaction analysis. The green colour = hydrogen bonding, pink color = ionic interaction, grey colour = hydrophobic interaction and blue colour = water bridges showed in Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp during 50 ns MD simulations.

opencc-byAug 2021View details →

Suppl Material- Pharmacokinetics of some newly synthesized 1, 5- benzothiazepine scaffolds: A molecular docking and molecular dynamics simulation approach

It is suppl material, table and figures for publications

opennotspecifiedMay 2022View details →

Fig. 4 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation

Fig. 4. Chemical structures of known compounds 7 32.

opennotspecifiedMay 2022View details →

Fig. 2 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation

Fig. 2. Key HMBC, COSY, and NOESY correlations of 1–6 and 9.

opennotspecifiedMay 2022View details →

Fig. 3 in PTP1B and α-glucosidase inhibitory activities of the chemical constituents from Hedera rhombea fruits: Kinetic analysis and molecular docking simulation

Fig. 3. Experimental and calculated ECD spectra of compounds 1–4.

opencc-by-4.0Dec 2023View details →

Dataset for "Identification of Potential inhibitors of the SARS-CoV2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations"

Open the record for dataset details and reuse information.

Figure 3 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021

Figure 3 Structure of naturally occurring coumarins 13–37 reported possessing antiviral activity.

Figure 2 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021

Figure 2 Structure of some coumarin drugs 4–13.

Figure 1 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021

Figure 1 Structure of Aminocoumarin antibiotics Novobiocin, Clorobiocin, and Coumermycin.

opencc-zeroApr 2023View details →

dryad24/100

Data for: Molecular docking simulation of FMP or N-FMP and FAPα

The data proves that a longer self-immolative linker of FMP improves the probe responsivity toward FAPα. To uncover the underlying mechanism, theoretical molecular docking simulation is further carried out to elucidate the different FAPα responsivity towards FMP and N-FMP by MolAICal 1.3. The X-ray crystal structure of FAPα from the Protein Data Bank (PDB code 1Z68) is used. 3D structures of FMP and N-FMP are obtained and energetically optimized by a ChemDraw 3D software. After molecular docking, FMP presents a strong hydrogen bond between the peptide substrate of the probe and FAPα residues at the site of Val540, Ser548, Gln547, Gly542, and Ser546 in the active pocket. By contrast, N-FMP shows relatively weak hydrogen bond interaction with only one site of FAPα at the Gln547 residue in the active pocket. The theoretical simulations indicate that the higher affinity of FAPα towards FMP and thus promotes the enzymatic cleavage efficiency relative to N-FMP, which is consistent well with the experimental results. Therefore, both theoretical simulations and experimental results confirm that FMP with the longer self-immolative linker has superior enzymatic kinetics for FAPα.