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Molecular docking and dynamics studies of curcumin with COVID-19 proteins.

ABSTRACT: Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. Curcumin, a natural bioactive molecule has been shown to have therapeutic potential for various diseases, and its effect on COVID-19 is also currently being explored. In this study, we show the binding potential of curcumin targeted to a variety of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), spike protein-ACE2 (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Furthermore, representative docking complexes were validated using molecular dynamics simulations and mechanistic studies at 100 ns was carried on nucleocapsid and nsp10 proteins with curcumin complexes which resulted in stable and efficient binding energies and correlated with that of docked binding energies of the complexes. Both the docking and simulation studies indicate that curcumin has the potential as an antiviral against COVID-19.

SUBMITTER: Suravajhala R

PROVIDER: S-EPMC8192041 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Molecular docking and dynamics studies of curcumin with COVID-19 proteins.

Suravajhala Renuka R Parashar Abhinav A Choudhir Gourav G Kumar Anuj A Malik Babita B Nagaraj Viswanathan Arun VA Padmanaban Govindarajan G Polavarapu Rathnagiri R Suravajhala Prashanth P Kishor P B Kavi PBK

Network modeling and analysis in health informatics and bioinformatics 20210610 1

Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanis ...[more]

PMID: 34131556

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Project description:With 19.3 million new cases and almost 10 million deaths in 2020, cancer has become a leading cause of death today. Curcumin and its analogues were found to have promising anticancer activity. Inspired by curcumin’s promising anticancer activity, we prepared three semi-synthetic analogues by chemically modifying the diketone function of curcumin to its pyrazole counterpart. The curcumin analogues (3a−c) were synthesized by two different methods, followed by their DFT analyses to study the HOMO/LUMO configuration to access the stability of compounds (∆E = 3.55 to 3.35 eV). The curcumin analogues (3a−c) were tested for antiproliferative activity against a total of five dozen cancer cell lines in a single (10 µM) and five dose (0.001 to 100 µM) assays. 3,5-Bis(4-hydroxy-3-methoxystyryl)-1H-pyrazole-1-yl-(phenoxy)ethanone (3b) and 3,5-bis(4-hydroxy-3-methoxystyryl)-1H-pyrazole-1-yl-(2,4-dichlorophenoxy)ethanone (3c) demonstrated the most promising antiproliferative activity against the cancer cell lines with growth inhibitions of 92.41% and 87.28%, respectively, in a high single dose of 10 µM and exhibited good antiproliferative activity (%GIs > 68%) against 54 out of 56 cancer cell lines and 54 out of 60 cell lines, respectively. The compound 3b and 3c demonstrated the most potent antiproliferative activity in a 5-dose assay with GI50 values ranging between 0.281 and 5.59 µM and 0.39 and 0.196 and 3.07 µM, respectively. The compound 3b demonstrated moderate selectivity against a leukemia panel with a selectivity ratio of 4.59. The HOMO-LUMO energy-gap (∆E) of the compounds in the order of 3a > 3b > 3c, was found to be in harmony with the anticancer activity in the order of 3c ≥ 3b > 3a. Following that, all of the curcumin analogues were molecular docked against EGFR, one of the most appealing targets for antiproliferative activity. In a molecular docking simulation, the ligand 3b exhibited three different types of interactions: H-bond, π-π-stacking and π-cationic. The ligand 3b displayed three H-bonds with the residues Met793 (with methoxy group), Lys875 (with phenolic group) and Asp855 (with methoxy group). The π-π-stacking interaction was observed between the phenyl (of phenoxy) and the residue Phe997, while π-cationic interaction was displayed between the phenyl (of curcumin) and the residue Arg841. Similarly, the ligand 3c displayed five H-bonds with the residue Met793 (with methoxy and phenolic groups), Lys845 (methoxy group), Cys797 (phenoxy oxygen), and Asp855 (phenolic group), as well as a halogen bond with residue Cys797 (chloro group). Furthermore, all the compound 3a−c demonstrated significant binding affinity (−6.003 to −7.957 kcal/mol) against the active site of EGFR. The curcumin analogues described in the current work might offer beneficial therapeutic intervention for the treatment and prevention of cancer. Future anticancer drug discovery programs can be expedited by further modifying these analogues to create new compounds with powerful anticancer potentials.

Project description:Curcumin is an extensively studied natural compound due to its extensive biological applications. However, there are some drawbacks linked to this compound such as poor absorption, low water-solubility, quick systemic elimination, fast metabolism, poor pharmacokinetics, low bioavailability, low penetration targeting efficacy and low stability. To overcome these drawbacks, curcumin is encapsulated in nano-carriers. In the current studies, we synthesized nanoparticles of curcumin without using nanocarriers by different methods such as nano-suspension (Cur-NSM), sonication (Cur-SM) and anti-solvent precipitation (Cur-ASP) to enhance the solubility of curcumin in water. The prepared nanoparticles were characterized by FTIR, SEM and XRD analysis. These curcumin nanoparticles were screened for their solubilities in water, DPPH scavenging, amylase, α-glucosidase and β-glucosidase enzymatic activities. The particle size of nano-curcumin was found to be in the 47.4-98.7 nm range. The reduction in particle size of curcumin dramatically increases its solubility in water to 79.2 μg mL-1, whereas the solubility of curcumin is just 0.98 μg mL-1. Cur-ASP showed the highest free radical scavenging potential (48.84 ± 0.98%) which was comparable with standard BHT (50.48 ± 1.11%) at 75.0 μg mL-1. As well, Cur-ASP showed the highest inhibition of α-amylase (68.67 ± 1.02%), α-glucosidase (58.30 ± 0.52%), and β-glucosidase (64.80 ± 0.43%) at 100 μg mL-1 which is comparable with standard drug acarbose. The greater surface area of nanoparticles exposes the various groups of curcumin for blocking the binding sites of enzymes. This strategy may be helpful in designing curcumin as a potent therapeutic agent against diabetes mellitus. Further, the molecular interactions of curcumin with α-amylase, α-glucosidase, β-glucosidase, and polyphenol oxidase were assessed by analyzing the plausible binding modes of curcumin in the binding pocket of each receptor. The best binding mode of curcumin was used to make complexes with the target proteins and their stability was confirmed by 50 ns MD simulation.

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Molecular docking and dynamics studies of curcumin with COVID-19 proteins.

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Molecular docking and dynamics studies of curcumin with COVID-19 proteins.

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