*3.2.3 ATP binding protein ComA (PDB: 3VX4)*

Quorum sensing is mediated by a signaling molecule autoinducer [53]. This system in some streptococcal species such as **S. mutans** is the ComABCDE pathway, in which inducing peptides are processed from the ComC precursor and exported to the extracellular space by ComA and ComB [43, 54]. ComA is a bifunctional ATP-binding cassette transporter comprising three domains: an N-terminal peptidase domain (PEP), a transmembrane domain, and a C-terminal nucleotide linker domain [55–57]. PEP is a peptidase belonging to the cysteine protease family [55, 58–60].

Docking with the ATP binding protein ComA PDB id: 3VX4 identified as the best ligands the compounds: licorisoflavan A (16) (Edock = −-132.56 kJ/mol), licoricidin (15) (Edock = −128.75 kJ/mol), and methoxyficifolinol (1) (Edock = −127.50 kJ/ mol). When observing the interactions of the best ligands in the formed complexes, it was observed that hydrogen bonds with residues Thr568 and Ser563 and steric interactions with Lys567 are common, indicating that these interactions contributed to the reduction of the interaction energy and stabilization of the complexes (**Figure 7**).

#### **Figure 7.**

*Representations of the interactions between the three best ligands (compounds 16, 15, and 1) and the amino acid residues of the ATP binding protein ComA PDB id: 3VX4. Blue dashed lines represent hydrogen bonds and red dashed lines represent steric interactions.*

*Molecular Docking of Phytochemicals against* Streptococcus mutans *Virulence Targets… DOI: http://dx.doi.org/10.5772/intechopen.101506*

#### **3.3 Exoenzymes**

#### *3.3.1 Glucanosyucrase (PDB id: 3AIC)*

Glucansucrases or glycosyltransferases (GTFs) are extracellular enzymes, produced by various bacteria, including **S. mutans**, that cleave sucrose into glucose and fructose and build sticky biofilm chains. The growth of the glucan chain was associated with adherence of one bacteria to another and the dental surface. Furthermore, modulate the diffusion of substances through the biofilm, which could occasionally serve as an extracellular energy reserve [61].

The glucanosucrase in *S. mutans* allows the metabolism of sucrose into lactic acid, which reduces the pH around the tooth, facilitating the dissolution of calcium phosphate from tooth enamel, which induces tooth decay [62]. These characteristics make the **S. mutans** glucanosucrase as one of the main and most studied targets for the development of new agents useful in the prevention of dental caries.

The best ligands that interacted with glucansucrase PDB id: 3AIC in the docking simulation were: erycrystagallin (10) (Edock = −145.72 kJ/mol), malvidin-3,5-diglucoside (20) (Edock = −138.84 kJ/mol), and erystagallin (11) (Edock = −136.44 kJ/ mol). Hydrogen bonds with residues Asp480, Asp481, Asn537, and steric interactions with residues Leu433, Glu515, and Trp517 are common to the two best ligands and seem to be important for reducing the energy of formation of these complexes (**Figure 8**).

The docking study conducted out by Kim et al. [63] between rubusoside and **S. mutans** glucanosucrase (PDB id: 3AIC), identified residues Leu 433, Leu434, Ala478, Asp480, Glu515, Trp517, and Tyr916 as the main ones involved in the stabilization of the complex, and validated these residues as important anchoring sites for potential inhibitors of this enzyme.

Bhagavathy, Mahendiran, and Kanchana [64], performed molecular docking between seven phytochemical isolates of *Psidium guajava* and *S. mutans* glucanosucrase (PDB id: 3AIB) and demonstrated that the main residues involved in the formation of the complexes were Thr426, Ile427, Gln553, and Tyr978. These residues diverged from those identified in this study.

#### **Figure 8.**

*Representations of the interactions between the three best ligands (compounds 10, 20, and 11) and the amino acid residues of the glucanoscarase PDB id: 3AIC. Blue dashed lines represent hydrogen bonds and red dashed lines represent steric interactions.*

Opposing, Islam et al. [65] performed a molecular docking study between epigallocatechin gallate (EGCG) and the same **S. mutans** enzyme, glucanosucrase (PDB id: 3AIB). The results showed that the main interactions that stabilize the complex of the ligand (EGCG) with the enzyme occurred between the amino acid residues Glu515 and Trp517, which were the same residues identified in our work, reinforcing the importance of these residues for the stabilization of the complex.

#### *3.3.2 Dextranase (PDB id: 3VMO)*

**S. mutans** dextranase is an enzyme that hydrolyzes the α-1,6 bonds of dextran and produces isomalto-oligosaccharides of different sizes for metabolic use [66, 67]. This protein is composed of 850 aa residues with a molecular mass of 94.5 kDa, but it has multiple native and recombinant forms [68, 69]. According to the sequencing of several enzymes in this family, dextranases are divided into five regions: a signal peptide sequence (N-terminal with 24 aa), a variable N-terminal region (Ser25-Asn99), a conserved region (Gln100-Ala615), a glucan binding site (Leu616-Ile732), and a C-terminal variable region (Asn733-Asp850) [70, 71].

Some biochemical studies, based on the comparison of amino acid sequences with other glycosyltransferases, revealed that the Asp385 residue is essential for the catalytic reaction [72]. Besides, it was observed that Asp270 from cycloisomalto oligosaccharide glucanotransferases from *Bacillus circulans* T3040 [73] and Asp243 from endodextranase from *Thermotoga lettingae* TMO [74], corresponding to Asp385 from dextranase from **Streptococcus mutans**, were recognized as **S. mutans** residues catalytic.

Molecular docking performed with the dextranase PDB id: 3VMO identified as the best ligands: licorisoflavan A (16) (Edock = −138.02 kJ/mol), malvidin-3,5-diglucoside (20) (Edock = −136.94 kJ μg/mol), and licoricidin (15) (Edock = −129.73 kJ/ mol). Compounds 15 and 16 showed steric interactions in common with residues Tyr257 and Ala559 and showed steric interactions and hydrogen bonds with the key residue Asp385 which has already been identified as essential for catalytic reaction. Diglucoside 20, on the other hand, had a lower energy conformation distinct from compounds 15 and 16 and interacted with other amino acid residues in the active site of the enzyme (**Figure 9**).

#### **Figure 9.**

*Representations of the interactions between the three best ligands (compounds 16, 20, and 15) and the amino acid residues of dextranase PDB id: 3VMO. Blue dashed lines represent hydrogen bonds and red dashed lines represent steric interactions.*

*Molecular Docking of Phytochemicals against* Streptococcus mutans *Virulence Targets… DOI: http://dx.doi.org/10.5772/intechopen.101506*

#### **Figure 10.**

*Representations of the interactions between the three best ligands (compounds 10, 11, and 1) and the amino acid residues of hemolysin PDB id: 2RK5. Blue dashed lines represent hydrogen bonds and red dashed lines represent steric interactions.*

#### *3.3.3 Hemolysin (PDB id: 2RK5)*

Hemolysins are exotoxins capable of promoting erythrocyte lysis. They are toxins produced by some species of streptococci [75] and contribute to the virulence process of **S. mutans** [76]. In **S. mutans***,* alpha- and gamma-hemolytic strains are described [77], as well as beta-hemolytic [78].

Docking with hemolysin PDB id: 3VMO identified as the best ligands the compounds: erycristagallin (10) (Edock = −112.64 kJ/mol), erystagallin (11) (Edock = −104.10 kJ/mol), and methoxyficifolinol (1) (Edock = −100.63 kJ/mol). The steric interactions and hydrogen bonds with Asn21, Asn24, and Asp30 residues were common for compounds 10 and 11, and seem to be important for the stabilization of the complexes. Compound 1, despite belonging to the same chemical class as compounds 10 and 11, showed a more stable conformation in another position of the active site, consequently, is stabilized by interactions with different amino acid residues, but which contributed less to the stabilization of the complex (**Figure 10**).
