The top 2 hybrids from Category 1 and 2 are sorted by the order of best to worst docking scores, and IFD values, IFD RMSD values, and MM/GBSA bind scores are mentioned
Name
Docking score at XP (kcal/mol)
IFD docking score at SP (kcal/mol)
IFD score (kcal/mol)
MM/GBSA dG bind energy (kcal/mol)
Category 1
23582824 (frag 1) + CNP0243567 (frag 44) NH-01
–13.354
–12.040
–2,079.60
–54.34
CNP0106688 (frag 9) + 70798655 (frag 1) NH-02
–12.661
–12.661
–2,080
–51.14
Category 2
56649450 (frag 9) + CNP0392152 (frag 1) NH-06
–12.67
–12.692
–2,083.46
–67.81
50990924 (frag 5) + CNP0475782 (frag 1) NH-07
–12.327
–13.022
–2,082.72
–72.66
IFD: induced fit docking; MM/GBSA: molecular mechanics/generalized Born and surface area; RMSD: root mean square deviation; SP: standard precision; XP: extra precision
The authors acknowledge Amity University Uttar Pradesh, Noida for providing the facilities for the conduct of the present study. The authors also acknowledge ICMR-DHR (R.12013/21/2023-HR/ E-Office: 8206474). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The authors declare that they have no conflicts of interest.
Ethical approval
Not applicable.
Consent to participate
Not applicable.
Consent to publication
Not applicable.
Availability of data and materials
Protein structure was retrieved from the RCSB-PDB website (https://www.rcsb.org/structure/8exl), PDB DOI: https://doi.org/10.2210/pdb8EXL/pdb. Natural compounds were accessed and downloaded from COCONUT databases at https://coconut.naturalproducts.net/ and drugs from Pubchem repository http://pubchem.ncbi.nlm.nih.gov/. The data generated and analyzed for this study are included in the manuscript and the supplementary files. Additional data should be requested from the corresponding author which may be provided on reasonable request and with a signed data access agreement.
Funding
This work was financially supported by ICMR-DHR [(R.12013/21/2023-HR/ E-Office: 8206474)]. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Open Exploration maintains a neutral stance on jurisdictional claims in published institutional affiliations and maps. All opinions expressed in this article are the personal views of the author(s) and do not represent the stance of the editorial team or the publisher.
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