Table 1.
Target proteins used in the study, their main functions, and associated pathway categories.
Fig 1.
Schematic of the computational workflow for the in-silico identification and validation of Mitoxantrone as a multitarget inhibitor of proteins implicated in ageing-associated cancers.
The pipeline consists of two main stages: (I) initial screening (steps 1-4), including data collection, preparation, multitargeted docking, and comparison to a control; and (II) detailed biophysical validation (steps 5-8), including DFT, WaterMap analysis, MD simulations, and MM-GBSA binding free energy calculations.
Fig 2.
The figure shows the prepared protein structures, their ligand binding sites, and the corresponding Ramachandran plots for the studied targets: A) Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), B) MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), C) mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and D) PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
Table 2.
Molecular docking scores (kcal/mol) and MM-GBSA binding energies (kcal/mol) for each target protein (PDB ID), including contributions from hydrogen bonds and vdW interactions.
Fig 3.
The figure shows the docked poses in a) 3D and b) 2D Ligand Interaction Diagrams for the studied targets in complex with identified compound Mitoxantrone (light pink) and control drug Doxorubicin (sweet leaf; greenish), with a legend indicating bond and residues and interaction types.
The interaction of both compounds with protiens are shown as A) Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), B) MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), C) mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and D) PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
Fig 4.
The figure shows the Molecular Interaction Fingerprints (MIFs) of docked poses of identified compound Mitoxantrone and Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
The count of interacting residues is shown as a bar on top, while the count of ligand interactions is shown at the right side of the plot.
Fig 5.
The figure shows the Density Functional Theory (DFT) Results of the identified compound Mitoxantrone, where the relative energy is shown along with all other energies.
Table 3.
Predicted pharmacokinetic and physicochemical parameters of Mitoxantrone and Doxorubicin computed using QikProp (Schrödinger v2024-4).
Fig 6.
WaterMap analysis of Mitoxantrone complexes with Mitoxantrone and Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3) showing 3D hydration (Aa–Da) and corresponding 2D residue interaction maps (Ab–Db).
The colour coding denotes residue properties and interaction types as indicated in the legend.
Fig 7.
The figure shows the Root Mean Square Deviation (RMSD) for Mitoxantrone in complex with A) Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), B) MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), C) mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and D) PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
Fig 8.
The figure shows the Root Mean Square Fluctuation (RMSF) for the studied targets in complex with Mitoxantrone, with a legend indicating fluctuations in protein residues and the green line representing ligand interactions: A) Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), B) MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), C) mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and D) PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
Fig 9.
The figure shows the Simulation Interaction Diagram (SID) and its histogram representation for the studied targets in complex with Mitoxantrone with Aa, Ab) Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), Ba, Bb) MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), Ca, Cb) mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and Da, Db) PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3).
Fig 10.
The figure shows the Binding Free and Total Complex Energy of Mitoxantrone in complex with Checkpoint kinase 1 (Chk1, PDB ID: 2YEX), MDM2 (Mouse double minute 2 homolog, PDB ID: 4HG7), mTOR (Mechanistic Target of Rapamycin kinase domain, PDB ID: 4JSX), and PARP-1 (Poly [ADP-ribose] polymerase 1 catalytic domain, PDB ID: 5DS3), computed on 100 ns MD Simulation Trajectories.