Molecular insight into binding behavior of polyphenol (rutin) with beta lactoglobulin: Spectroscopic, molecular docking and MD simulation studies

Al‐Shabib, Nasser Abdulatif; Khan, Javed Masood; Malik, Ajamaluddin; Alsenaidy, Mohammad A.; Rehman, Tabish; Alajmi, Mohamed F.; Al-Senaidy, Abdulrahman M.; Husain, Fohad Mabood; Khan, Rizwan Hasan

doi:10.1016/j.molliq.2018.07.122

Cited by 131 publications

(78 citation statements)

References 42 publications

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“…MD simulation provides information regarding the time dependent behavior of any molecular system by integrating Newton's laws of motion (Mandlik and Singh, 2016). The stability of the docked complexes were determined by performing an MD simulation as previously described (Al-Shabib et al, 2018;AlAjmi et al, 2018). The protein-ligand root mean square deviation (PL-RMSD) was used to measure the scaler distance between M pro and the ligands throughout the trajectory (100 nsecs) and also to evaluate the evolvement of the Ca protein backbone as well as the protein and ligand RMSD over the course of 100 nsecs period.…”

Section: Molecular Dynamic Analysismentioning

confidence: 99%

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

Fadaka

Aruleba

Sibuyi

et al. 2020

Journal of Biomolecular Structure and Dynamics

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The exponential increase in cases and mortality of coronavirus disease (COVID-19) has called for a need to develop drugs to treat this infection. Using in silico and molecular docking approaches, this study investigated the inhibitory effects of Pradimicin A, Lamivudine, Plerixafor and Lopinavir against SARS-CoV-2 M pro. ADME/Tox of the ligands, pharmacophore hypothesis of the co-crystalized ligand and the receptor, and docking studies were carried out on different modules of Schrodinger (2019-4) Maestro v12.2. Among the ligands subjected to ADME/Tox by QikProp, Lamivudine demonstrated drug-like physico-chemical properties. A total of five pharmacophore binding sites (A3, A4, R9, R10, and R11) were predicted from the co-crystalized ligand and the binding cavity of the SARS-CoV-2 M pro. The docking result showed that Lopinavir and Lamivudine bind with a higher affinity and lower free energy than the standard ligand having a glide score of À9.2 kcal/mol and À5.3 kcal/mol, respectively. Plerixafor and Pradimicin A have a glide score of À3.7 kcal/mol and À2.4 kcal/mol, respectively, which is lower than the co-crystallized ligand with a glide score of À5.3 kcal/mol. Molecular dynamics confirmed that the ligands maintained their interaction with the protein with lower RMSD fluctuations over the trajectory period of 100 nsecs and that GLU166 residue is pivotal for binding. On the whole, present study specifies the repurposing aptitude of these molecules as inhibitors of SARS-CoV-2 M pro with higher binding scores and forms energetically stable complexes with M pro .

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Section: Molecular Dynamic Analysismentioning

confidence: 99%

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

Fadaka

Aruleba

Sibuyi

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…The average RMSD values of the Piperine bound proteins as compared to only proteins are found to be less representing to their conformational stability. Both the simulations are attained equilibrium within 0.3 nm, which is also a measure of the systems’ stability during the simulation (Al-Shabib et al., 2018 , 2020 ; Millan et al., 2018 ).…”

Section: Resultsmentioning

confidence: 99%

In silicoinvestigation of spice molecules as potent inhibitor of SARS-CoV-2

Rout

Swain

Tripathy

2020

Journal of Biomolecular Structure and Dynamics

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel infectious disease that is in rapid growth. Several trials are going on worldwide to find a solution for this pandemic. The viral replication can be blocked by inhibiting the receptor-binding domain (RBD) of SARS-CoV-2 spike protein (SARS-CoV-2 RBD Spro) and the SARS-CoV-2 main protease (SARS-CoV-2 Mpro). The binding of potential small molecules to these proteins can inhibit the replication and transcription of the virus. The spice molecules that are used in our food have antiviral, antifungal and antimicrobial properties. As spice molecules are consumed in the diet, hence its antiviral properties against SARS-CoV-2 will benefit in a significant manner. Therefore, in this work, the molecular docking of 30 selected spice molecules (screened through ADME property) was performed to identify the potential inhibitors for the RBD Spro and Mpro of SARS-CoV-2. We have found that though all the molecules bind actively with the SARS-CoV-2 RBD Spro and Mpro, but Piperine has the highest binding affinity among the 30 screened molecules. Besides, the comparative study between Piperine and currently used drugs show that Piperine is more effective. The interaction of Piperine with RBD Spro and Mpro is further validated by the molecular dynamics (MD) simulation studies. The free energy landscape and binding free energy results also, support for the stable complex formation of Piperine with RBD Spro and Mpro. We anticipate immediate wet-lab experiments and clinical trials in support of this computational study that might help to inhibit the SARS-CoV-2 virus.

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“…To visualize the interaction between C 16 C 4 C 16 Br 2 and BLC, molecular docking was performed using AutoDock4.2 as described previously. 31 The 2D structure of C 16 C 4 C 16 Br 2 was drawn using the Sketcher module in "Maestro-2018 (Schrodinger, LLC, NY, USA)" and its energy was minimized using the OPLS3e forceeld. The ionization state of C 16 C 4 C 16 Br 2 was generated at pH 7.4 using Epik-2018 (Schrodinger, LLC, NY, USA).…”

Section: Molecular Dockingmentioning

confidence: 99%

“…Molecular dynamics simulation C 16 C 4 C 16 Br 2 was evaluated by performing a molecular dynamics simulation using Desmond-2018 (Schrodinger, LLC, NY, USA) as reported previously. 31 Briey, the BLC-C 16 C 4 C 16 Br 2 complex was placed at the center of an orthorhombic simulation box, and at least 1 nm away from the box boundaries. The simulation box was solvated with TIP3P water molecules and counterions were added to neutralize the system.…”

Section: Molecular Dockingmentioning

confidence: 99%

Cationic gemini surfactant stimulates amyloid fibril formation in bovine liver catalase at physiological pH. A biophysical study

et al. 2020

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Molecular insight into binding behavior of polyphenol (rutin) with beta lactoglobulin: Spectroscopic, molecular docking and MD simulation studies

Cited by 131 publications

References 42 publications

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

In silicoinvestigation of spice molecules as potent inhibitor of SARS-CoV-2

Cationic gemini surfactant stimulates amyloid fibril formation in bovine liver catalase at physiological pH. A biophysical study

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