## 4 Computer-Aided Molecular Design (CAMD) of Coumarins for Potential Plant Protection Application
### Molecular Docking, and Molecular Dynamics (MD) Simulations  
Molecular docking and MS simulation study of 3-hydroxycoumarin as inhibitors of the fungus _Moniliophthora perriciosa_, the causal agent of witches' broom disease in _Theobroma cacao_ L., shows that their antifungal activity is based on the inhibition of chitin synthase (CS). CS' active site predominates residues for hydrogen bond acceptors. Also, the low hydrophobicity of the active site of CS, favors 3-hydroxycoumarin, due to the hydroxyl groups [33].  
In order to determine the possible mechanism of action of coumarins [35] and coumarinyl Schiff bases [36] against pathogenic fungi [PERSON] et al. have performed molecular docking studies on three enzymes responsible for the fungal growth: demethylase (sterol 14\(\alpha\)-demethylase (CYP51), pdb ID: 5 eah) [137]; chitinase (pdb ID: 4 txe) [138]; transferase (\(N\)-myristoyltransferase, pdb ID: 2p6g) [139]; and the three plant cell wall-degrading en zymes: endoglucanase I (pdb ID:20 vw) [140]; proteinase K (pdb ID: 2 pwb) [141]; pectinase (endopolygalacturonase, pdb ID:1 czf) [142]. The results of molecular docking suggest that tested coumarins may act against S. sclerootomy as inhibitors of proteinase K and pectinase. The results of the molecular docking study are in agreement with the results of the study conducted by [PERSON] et al. [143], which proved that S. sclerootomy, destroys plant tissues during infection by various enzymes, such as proteinases.  
The most active coumarin forms four strong hydrogen bonds in the binding site of proteinase K (Figure 8): oxygen atoms from the 6-OH group with Ala172; oxygen atoms from the 3-carbonyl group with Ser224 and Thr223, and oxygen atoms from the 2-keto group with Asn161, which indicates the importance of groups with electronegative atoms from hydroxyl and acetyl groups for enhanced antifungal effects of coumarin derivatives. Molecular docking has shown that coumarins [35] and coumarinly Schiff bases [36] possibly act against _M. phaseolina_ as inhibitors of endoglucanase and pectinase.  
The binding modes between acetylcholinesterase (AChE, pdb:1 odc), one of the targets of nematode _Meloidogyne incognita_, and the novel chromosome derivatives were defined using molecular docking. The docking results indicated that the two most active compounds interact with amino acid residues Tyr121, Trp279, Tyr70, Trp84, and Phe330 of AChE via hydrogen bond and \(\pi\)-\(\pi\) stacking [144]. Also, molecular docking and molecular dynamics show that the strong and stable binding of coumarin derivatives to AChE can be attributed to their strong inhibitory potential [35; 36; 145]. DNA gyrase (EC 5.6.2.2) is a type II topoisomerase that catalyses changes in topology of DNA i.e., an enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA. It is an essential bacterial enzyme but absent from higher eukaryotes, making it an attractive target for antibacterial activities. Targeting DNA gyrase with an inhibitor disrupts DNA synthesis, leading to cell death [146]. Using in silico analysis, heterocyclic compounds containing coumarin scaffolds have been proposed as bacterial DNA gyrase inhibitors [147].  
The molecular docking has demonstrated a high affinity of scopoletin to the nucleotide-binding pocket of TcPMTCA1, forming five hydrogen bonds: between the 7-hydroxy with Src297, 6-methoxy with Ala298, oxygen at position 1 with Lys301, and oxygen at position 2 with Lys301 and Ser300 [136]. Molecular docking of phenolic ether derivatives of scopoletin  
Figure 8: Hydrophobic surface representation of proteinase K active site with docked coumarin [35].  
with TcPMA1 demonstrates that derivatives with shorter side chains at the 7-position interact with more key amino acid residues than scopoletin [133]. Results of computational methods helped to elucidate TcPMA1-mediated detoxification mechanisms of scopoletin and other coumarin derivatives, providing valuable information for the design of novel PMCA-inhibiting acaricides [136].