Molecular Docking and Chemical Analysis of Alcohol Compounds ( C 16C 20 ) Bound to InhA Receptors as Mycobactericidal Candidates

Received: 24 October 2019 Revised: 6th April 2020 Accepted: 7th April 2020 Online: 31th May 2020 Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis. TB infection spreads through the air and is more likely when using inappropriate disinfectants in medical and laboratory equipment related to TB research. Appropriate disinfectants used for laboratory equipment can reduce the risk of TB disease transmission. Alcohol compound is a common disinfectant with broadspectrum activity against microbes, viruses, and fungi. Molecular Docking can be applied to support virtual receptor-ligand screening in finding the right mycobactericidal agent as a disinfectant candidate from the alcohol group. Based on docking analysis, octadecanol (Gs) has potential as a mycobactericidal agent with InhA as its specific receptor. Gibbs (AG) free energy obtained by octadecanol (Cis) and InhA is -4.9 kcal/mol.


Introduction
Based on data from the World Health Organization (WHO), in 2018, tuberculosis (TB) is still included in the top ten diseases that cause death. In 2017 , 10 million people were affected by TB, and 1.6 million died from this disease (including 0.3 million of those affected by HIV). In the same year, an estimated 1 million children were affected by TB, and 230 ,000 children died from this disease (including those affected by HIV). TB is the main killer in people suffering from HIV-positive. Tuberculosis with Multi-Drug Resistance (MDR) causes a public health crisis and threatens health security. WHO estimates there are 558 ,000 new cases with resistance to rifampicin ( the most effective first-line drug, 82%). In 2010, a school in South India reported tuberculosis (TB) infection in nurse candidates [1]. Besides, research in Lima, Peru, has revealed the potential presence of TB infection in the Emergency Department (ED). Several public places have also been reported as sites of infection, including hospitals [2] and orphanages [ 3 ].
TB infection spreads through the air and can also spread when using inappropriate disinfectants on medical equipment used for TB research in laboratories [ 4 ]. Appropriate disinfectants should be used in laboratory equipment to reduce the risk of TB transmission [ 5 , 6]. This research is essential in investigating the most effective disinfectants as mycobactericidal agents through the reaction of several mycobactericidal compounds to M. tuberculosis. Uniquely, the structure of M. tuberculosis cell walls has hydrophobic properties and is more resistant to biocides compared to other bacteria, so that these bacteria can live longer in specific environments [ 7 , 8, 9 , 10].
Alcoholic compounds and their derivatives have been shown to have antimycobacterial activity [11,12,13 ]. The antimycobacterial activity of alcohol compounds is influenced by the number of carbon chains (C), polarity, double bonds, and triple bonds in the structure of alcohol [ 14 ]. Previous studies reported that alcohols with 7 -10 carbon atoms have antimycobacterial potential, whereas C10 (l-decanol) has the best ability to inhibit M. bovis and M. tuberculosis [ 15 ]. However, there is little research on the effect of alcohol as a disinfectant. In general, alcohol is known to damage cell membranes and denature proteins that affect cell metabolism and lysis [16].
Several enzymes involved in TB cell wall biosynthesis are attractive targets in the design of g antituberculosis drug compounds [ 17 ]. The function of the enoyl-acyl carrier protein reductase (InhA) is to catalyze the process of reducing the 2-trans-enoyl carbon chain with at least 12 carbon chains. This enzyme is responsible for the final process of every carbon extension in the biosynthesis of fatty acids. InhA is involved in the production of long-chain fatty acids and mycolic acids, which makes it an attractive target in the design of inhibitors to inhibit the biosynthesis of fatty acid chains in the cell wall of M. tuberculosis [18, 19 , 20].
Drug discovery and design are processes that involve many scientific disciplines such as drug chemistry, pharmacology, biochemistry, and computational biology. Previously, the researchers did it through an experimental process that was a barrier to drug development because it took time and money. At present, computational methods supporting the drug design process are becoming more efficacious [21,22]. The virtual screening process involves drug design and computer-aided development (CADDD) methods. The virtual screening method uses molecular docking simulation to illustrate the orientation of small molecules that bind to the target protein based on the calculation of the value of activity and affinity [   (e) C20 and (f ) isoniazid (g) triclosan (h) mycolic acid

. Receptor Preparation
The three-dimensional ( 3 D) structure of the target receptor or enzyme (InhA) was obtained from the Protein Data Bank (PDB) (https: // www.rscb / pdb.org) [28]. The crystal structure for InhA used in this study was PDB ID: 2B 37 . Based on previous research, residual binding sites for InhA were identified and presented in Table 1[18, 29 ]. The InhA structure is visualized in Figure 2: Determining the right disinfectant is significant for controlling the spread of infectious diseases in public places [26]. Research on molecular Docking of alcohol compounds with the InhA receptor as an appropriate disinfectant to eradicate M. tuberculosis growth has been carried out by [ 27 ]. The study focused on alcohol compounds (C 1-C 15 ) only, and the results showed that Ci5 has the potential as a mycobactericidal agent with a Gibbs free energy value ( AG) of -4.9 kcal / mol. This study examines the potential of alcohol compounds with a longer C atom (C 16-C20 ) as a mycobactericidal agent.

Equipment and Materials
Computational visualization and molecular docking analysis were performed using PyMol software, Visual Molecular Dynamics (VMD), and Ligplot Plus. Meanwhi/e, the hardware used is Lenovo Ideapad 330 Laptop with AMD A 9 -9425 processor, 4 GB RAM, and 1 TB hard disk and using Windows 10 as the operating system.

Ligand Preparation
Alcohol compounds (C 16-C20 ), Isoniazid, triclosan and mycolic acid were selected for docking analysis, and the structure was taken from the PubChem chemical structure database (https: // pubchem.ncbi.nlm.nih.gov / ). Isoniazid is a drug for the treatment of TB. Triclosan is a common ingredient in disinfectant products, whl/e mycolic acid is a natural ligand from the InhA protein.
Isoniazid and triclosan were used in comparing mycobactericidal activity with alcohol compounds used in this study. All chemical structures were stored in PDB format. Previously, all ligands were optimized for their structures using Marvin Sketch software in which the optimal structures are presented in Figure 1:

. Gibbs free energy ( AG)
Molecular Docking is carried out on an alcohol compound (C 16-C20) against the InhA receptor. Molecular Docking is advantageous for virtual filtering of the potential inhibition of alcohol compounds to the receptors. The potential of alcohol is shown by Gibbs free energy ( AG) from the results of molecular Docking. Gibbs's free energy value ( AG), which is more negative, indicates binding energy, which is more stable and stronger on ligands and receptors.

. Ligand-Receptor Interaction
The Gibbs free energy data ( AG) in Table 2 shows that octadecanol is the strongest ligand in inhibiting InhA ( AG = -4.9 kcal / mol) compared to other alcohol compounds, whf /e heptadecanol is the weakest ligand ( AG = -4.2 kcal / mol).

.1. Octadecanol-InhA
Among the five alcohol compounds docking with InhA, octadecanol was found to have Gibbs free energy ( AG = -4.9 kcal / mol), which was more negative than other ligands.
nel94 UnkO Pro193 Table 2 shows the Gibbs free energy ( AG) obtained from the Lamarckian Genetic Algorithm (LGA) calculation on the AutoDock Vina. Gibbs free energy values ( AG) reveal that alcohol compounds have more potential in inhibiting InhA. It is observed that the longer chain of carbon atoms in alcohol produces higher binding energy, which is characterized by the  (Table 1).
Octadecanol is an alcohol compound with 18 C atoms and creates hydrophobic interactions with the InhA residue is lie 215 , Leu2i8, Meti 99 , Phe 149 , lie 194 , Proi 93 , Aspi 48 , G/yi 92 , G/yi 92 , A/ai 9 i, Me/ 147 , lie21, Tyn. 58 . The presence of hydrogen bonds is found in interactions between octadecanol and InhA. Hydrogen bonding occurs between Proi 56 and the hydroxy group present in octadecanol ( Cis ) with a length of 3.01 A. The hydrogen bond occurs between the 0 atom in the Proi 56 hydroxy group and the 0 atom in the octadecanol ( Cis ) hydroxy group. Orientation and interaction of pentadecanol when binding with InhA is illustrated in Figures 1 and 2. All potential ligands are bound at the binding site of each receptor, where the residue at the binding site is the best residue for docking ligands (Figure 3 -4 ).
Furthermore, the ligand interacts with other residues in each receptor that affects the energy configuration in the receptor-ligand complex ( Table 2). Previous studies mention the influence of the C atom [ 27 ], which states that Pentadecanol, which has fifteen rotational bonds on the compound , gives the effect and orientation on the InhA binding side. This also happens to octadecanol because it has a rotational bond that affects the orientation of octadecanol on the InhA binding side. In addition, the hydrophobic effect of increasingly negative value of AG) between the ligand and the receptor. For instance, the binding energy for octadecanol-InhA is AG -4.9 kcal / mol, for hexadecanol-InhA AG = -4.5 kcal / mol, and so on. Compared with Isoniazid, the C10-C 15 alcohol compound almost has the same ability as an InhA inhibitor where the binding energy is -4.2 kcal / mol.
Unlike the triclosan binding energy as an inhibitor, receptors are relatively more reliable than alcohol compounds. The triclosan affinity energy with InhA is -6.4 kcal / mol. Because the binding energy of alcohol is between Isoniazid and triclosan, it is concluded that this type of alcohol (C 16 -C20) has the ability to inhibit InhA. amino acids around the ligand influences the orientation and binding energy of octadecanol on the InhA binding site. Van der Walls energy has a binding energy of 40 kj / mol [ 30 ]. These results indicate that octadecanol has potential as an inhibitor in the InhA enzymatic reaction. This results in the potential of InhA as an enzyme that helps the genus Mycobacterium's energy supply be inhibited , resulting in reduced bacterial growth. hydrogen bonds found in interactions between mycolic acid and InhA. Hydrogen bonds that occur between G/ 3 /96 with a hydroxy group in mycolic acid compounds with a length of 3.12 A. The hydrogen bond occurs between the 0 atom in the G/y 96 group and the 0 atom in mycolic acid. The orientation and interaction of mycic acid when binding to InhA is illustrated in Figures 5 and 6.

.2. Mycolic acid -InhA
In addition to the alcohol compound docking with InhA, mycolic acid was found to have more negative Gibbs ( AG) free energy than other ligands ( AG = -5.9 kcal / mol) ( Table 2).

. 3 . Triclosan-InhA
Triclosan bound to InhA is a comparative ligand used as an active disinfectant. It has the best Gibbs free energy value, among other test ligands (-6.4 kcal / mol).

. 4 . Isoniazid-InhA
Based on the data obtained, Isoniazid, which is a tuberculosis drug that is commonly used, has a Gibbs free energy value of -4.2 kcal / mol. Isoniazid has 6 C atoms and creates hydrophobic interactions with the InhA residue, i.e., Proi 93 , Ite2i, Alaigi , G/ 3 /192, Phe 149 , Aspi 48 . The presence of hydrogen bonds is found in interactions between Isoniazid and InhA. The hydrogen bond that occurs between lie 194 and the amine group present in the isoniazid compound has a bond length of 2.95 A and 3.07 A. The hydrogen bond occurs between the 0 and N atoms in the lie 194 group and the N atoms in Isoniazid. The orientation and interaction of Isoniazid when binding to InhA is illustrated in Figures 9 and 10.

. Conclusion
Based on the Molecular Docking study, the right disinfectant is influenced by several factors; 1) receptors as targets of the inhibition process, 2) ligands as inhibitors, 3 ) stability of interactions between receptors and ligands. Based on Molecular Docking, the C 15 -C20 alcohol compound has potential as a mycobactericidal agent. From the study of alcohols with C16 to C20, it is found that Octadecanol is more appropriate as a mycobactericidal agent because of its inhibitory activity against the InhA receptor.