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- Cancer therapy faces challenges due to drug resistance and signaling pathway redundancy, allowing cancer cells to evade treatment. Dual inhibition of Src homology region 2 domain-containing phosphatase-2 (SHP2) and heat shock protein 90 (HSP90) offers a promising strategy to overcome these limitations. We evaluated neem-derived compounds against SHP2 (PDB ID: 5EHR) and HSP90 (PDB ID: 1YET) using molecular docking, hierarchical clustering, and structural similarity analyses. Drug-likeness was assessed using Lipinski's rule of five, and Tanimoto similarity coefficients were calculated. Nimbocinol, nimbidin, and margolone showed promising binding affinities to both targets. Nimbocinol demonstrated superior binding to SHP2 (-10.463kcal/mol) compared to SHP099 (-10.009kcal/mol). Margolone formed specific interactions, including a salt bridge between its carboxylate group and His100 in HSP90. All compounds complied with Lipinski's rule, with margolone showing structural similarities to geldanamycin and SHP099. This study identifies neem-derived compounds as potential dual inhibitors of SHP2 and HSP90, presenting a paradigm shift in cancer therapeutic strategy. These findings provide a foundation for developing novel multi-targeted anticancer therapeutics.
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- Orexinergic system dysfunction is the fundamental basis for several neurological illnesses like narcolepsy, insomnia, and drug dependency, yet none of the existing medications are subtype receptor specific. This study examines 124 chemicals from neem to determine if they can be utilised as specific orexinergic receptor modulators using advanced computational methods. The methodology includes detailed clustering, pharmacophoric interaction, pharmacokinetic, statistical, and clustering analyses. Molecular property profiling indicated the majority of the compounds exhibit excellent drug-like qualities (MW 350-450 Da, LogP 0-2), while principal component analysis captured 100% structural variability between two components (92.5% and 7.5%, respectively). Molecular docking simulations indicated selective binding to the 6V9S receptor (-11.3 to -4 kcal/mol) over 4S0V (-9.7 to -4 kcal/mol). Lead compounds Neem_PDB_10257 (Tirucallol) (-11.3 kcal/mol) and Neem_PDB_12072821 ([(5 R,7 R,8 R,9 R,10 R,13S,17 R) -17-(2-methoxy-5-oxo-4,4,8,10,13-pentamethyl-3-oxo-5,6,7,9,11,12,16,17-octahydrocyclopenta[a]phenanthren-7-yl] acetate) were particularly 6V9S selective (>2 kcal/mol difference), whereas Neem_PDB_10160319 ((4S,4aS,5S,10S,13S,14S,17-4,4,10,13,14-pentam -1, 2, 3, 5, 6, 7, 11, 12, 15, 17-decahydrocyclopenta[a]phenanthren-16-one) was most sensitive towards 4S0V. Two top-ranked compound families were discovered by hierarchical cluster analysis with a distance requirement of 35 units, and receptor-specific dendrograms revealed distinctive subcluster branching patterns (4S0V: 5.5 and 6.7 unit subclusters; 6V9S: 7.1 and 7.2 unit subclusters). Interaction pattern (heatmap analysis) identified major interaction hotspots, including TYR348, TRP120, PHE227, and HIS350. Neem_PDB_163184214 (Meliatetraolenone) specifically targeted ASN318 in 6V9S, while Neem_PDB_54580354 (7-Benzoylnimbocinol) favored interaction with GLN134 in 4S0V (>90 interactions). These findings dispute the "one-pharmacophore" theory for orexinergic modulators, showing that intentional functionalization of NEM templates can deliver subtype-selective treatments with maximal sleep-wake modulation and low off-target effects.
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