tetano
Editor, Senior Moderator
Sci Rep
. 2025 Nov 7;15(1):39099.
doi: 10.1038/s41598-025-24162-w. Insights from integrated covalent docking and molecular dynamics simulations of nirmatrelvir analogs as potential SARS-CoV-2 M[SUP]pro[/SUP] inhibitors
Mahmoud A A Ibrahim[SUP] 1 2 3 [/SUP], Doaa M A Khaled[SUP] 4 [/SUP], Doaa G M Mahmoud[SUP] 4 [/SUP], Alaa H M Abdelrahman[SUP] 4 [/SUP], Peter A Sidhom[SUP] 5 [/SUP], Yanshuo Han[SUP] 6 [/SUP], Tamer Shoeib[SUP] 7 [/SUP], Badr Aldahmash[SUP] 8 [/SUP], Ahmed Rady[SUP] 8 [/SUP]
Affiliations
The COVID-19 epidemic has posed a considerable challenge to the worldwide economy and public health, underscoring the crucial demand for developing effective antiviral medications. The SARS-CoV-2 main protease (M[SUP]pro[/SUP]) is a vital enzyme for antiviral drugs because of its fundamental function in viral reproduction. Nirmatrelvir (PF-07321332), a nitrile-based covalent ligand of M[SUP]pro[/SUP], has garnered significant interest because it demonstrates additive efficacy when co-administered with ritonavir and is known as Paxlovid. Herein, forty-five nirmatrelvir analogs collected from the PubChem database were mined against M[SUP]pro[/SUP] utilizing covalent docking computations. Initially, the reliability of the AutoDock4.2.6 software in predicting M[SUP]pro[/SUP]-ligand binding modes was validated based on accessible experimental data. Nirmatrelvir analogs with binding scores lower than nirmatrelvir (calc. -13.3 kcal/mol) were advanced for molecular dynamics simulations (MDS), accompanied by binding energy assessments performed via the MM-GBSA approach. Based on MM-GBSA//100 ns MDS, PubChem-162-396-453, PubChem-162-396-449, and PubChem-162-396-448 exhibited superior binding affinities with ΔG[SUB]binding[/SUB] values of -49.7, -46.3, and -44.9 kcal/mol, respectively, compared to nirmatrelvir (ΔG[SUB]binding[/SUB] = -40.7 kcal/mol). The identified analogs demonstrated significant structural and energetic stability within M[SUP]pro[/SUP] throughout 100 ns MDS. Evaluations of their drug-likeness and pharmacokinetic properties disclosed desirable oral bioavailability. The in-silico outcomes suggested that the identified analogs unveiled high potency as M[SUP]pro[/SUP] inhibitors, highlighting the necessity for follow-up in-vitro/in-vivo evaluations to assess their efficacy as anti-COVID-19 agents.
Keywords: COVID-19; Molecular dynamics; Nirmatrelvir analogs; Reversible covalent docking; SARS-CoV-2 Mpro.
. 2025 Nov 7;15(1):39099.
doi: 10.1038/s41598-025-24162-w. Insights from integrated covalent docking and molecular dynamics simulations of nirmatrelvir analogs as potential SARS-CoV-2 M[SUP]pro[/SUP] inhibitors
Mahmoud A A Ibrahim[SUP] 1 2 3 [/SUP], Doaa M A Khaled[SUP] 4 [/SUP], Doaa G M Mahmoud[SUP] 4 [/SUP], Alaa H M Abdelrahman[SUP] 4 [/SUP], Peter A Sidhom[SUP] 5 [/SUP], Yanshuo Han[SUP] 6 [/SUP], Tamer Shoeib[SUP] 7 [/SUP], Badr Aldahmash[SUP] 8 [/SUP], Ahmed Rady[SUP] 8 [/SUP]
Affiliations
- PMID: 41203702
- PMCID: PMC12594805
- DOI: 10.1038/s41598-025-24162-w
The COVID-19 epidemic has posed a considerable challenge to the worldwide economy and public health, underscoring the crucial demand for developing effective antiviral medications. The SARS-CoV-2 main protease (M[SUP]pro[/SUP]) is a vital enzyme for antiviral drugs because of its fundamental function in viral reproduction. Nirmatrelvir (PF-07321332), a nitrile-based covalent ligand of M[SUP]pro[/SUP], has garnered significant interest because it demonstrates additive efficacy when co-administered with ritonavir and is known as Paxlovid. Herein, forty-five nirmatrelvir analogs collected from the PubChem database were mined against M[SUP]pro[/SUP] utilizing covalent docking computations. Initially, the reliability of the AutoDock4.2.6 software in predicting M[SUP]pro[/SUP]-ligand binding modes was validated based on accessible experimental data. Nirmatrelvir analogs with binding scores lower than nirmatrelvir (calc. -13.3 kcal/mol) were advanced for molecular dynamics simulations (MDS), accompanied by binding energy assessments performed via the MM-GBSA approach. Based on MM-GBSA//100 ns MDS, PubChem-162-396-453, PubChem-162-396-449, and PubChem-162-396-448 exhibited superior binding affinities with ΔG[SUB]binding[/SUB] values of -49.7, -46.3, and -44.9 kcal/mol, respectively, compared to nirmatrelvir (ΔG[SUB]binding[/SUB] = -40.7 kcal/mol). The identified analogs demonstrated significant structural and energetic stability within M[SUP]pro[/SUP] throughout 100 ns MDS. Evaluations of their drug-likeness and pharmacokinetic properties disclosed desirable oral bioavailability. The in-silico outcomes suggested that the identified analogs unveiled high potency as M[SUP]pro[/SUP] inhibitors, highlighting the necessity for follow-up in-vitro/in-vivo evaluations to assess their efficacy as anti-COVID-19 agents.
Keywords: COVID-19; Molecular dynamics; Nirmatrelvir analogs; Reversible covalent docking; SARS-CoV-2 Mpro.