IN SILICO DOCKING STUDY OF MYCOBACTERIUM TUBERCULOSIS RV1250 PROTEIN USING ISONIAZID AND A NOVEL MODELED COMPOUND

Аннотация

Tuberculosis (TB) remains a major global health threat, largely due to the emergence of drug-resistant strains of Mycobacterium tuberculosis. Identifying novel molecular targets is critical for thedevelopment ofnew therapeutic agents. In this study, theRv1250 efflux protein of M. tuberculosis was selected as a potential drug target. Molecular docking analysis was conducted using AutoDock Vina to evaluate the binding affinity of two ligands: isoniazid, a known anti-TB drug, and a newly designed in silicocompound. The docking results revealed that the novel compound exhibited a binding affinity of –8.0 kcal/mol, which is more favorable than that of isoniazid (–6.1 kcal/mol). The new ligand formed stronger hydrogen bonds and hydrophobic interactions within theactive siteoftheRv1250 protein. Thesefindings suggest that the novel molecule may serve as a potential inhibitor of Rv1250 and warrants further biological investigation. Keywords: Mycobacterium tuberculosis, Rv1250 protein, isoniazid, molecular docking, AutoDock Vina, in silico design 1.Introduction Tuberculosis (TB) is a highly infectious disease that poses a serious global health threat, affecting more than 10 million people annually. The primary causative agent, Mycobacterium tuberculosis, has become increasingly difficult to treat due to the widespread emergence of antibiotic-resistant strains. According to the World Health Organization (WHO), TB was responsible for over 1.6 million deaths in 2021 alone. Isoniazid, a first-line anti-TB drug, acts by inhibiting the biosynthesis of mycolic acids, which are essential components of the bacterial cell wall. However, the growing incidence of isoniazid resistance has created an urgent need for novel bioactive compounds. In silico approaches, particularly molecular docking, are widely used to identify new drug candidates and to overcome microbial resistance. These computational methods help predict the binding interactions between small molecules and target proteins. The Rv1250 protein of M. tuberculosis, a member of the major facilitator superfamily (MFS), is considered a potential drug target due to its role in efflux-mediated antibiotic resistance. In the present study, we performed molecular docking using AutoDock Vina to analyze the interactions of the Rv1250 protein with two ligands: isoniazid, a known anti-TB agent, and a newly modeled compound. The binding affinities and interaction patterns with key amino acid residues were examined to evaluate thepotential ofthenovel ligand as aTB therapeuticcandidate. 2.Materials andMethods 2.1.Preparation ofTarget Protein The target protein used in this study was the Mycobacterium tuberculosis Rv1250 protein, an efflux transporter belonging to the Major Facilitator Superfamily (MFS). Its crystallographic structure was retrieved from the Protein Data Bank (PDB ID: 6G9X) in .pdb format. To prepare the protein for docking simulations, the structure was cleaned using AutoDock Tools (ADT) version 1.5.6. This included the removal of non-essential components such as crystallographic www.wordlyknowledge.uz ILMIYMETODIK JURNAL JOURNAL OFIQRO –ЖУРНАЛ ИҚРО –IQRO JURNALI –volume 16,issue02,2025 ISSN:2181-4341, IMPACT FACTOR( RESEARCH BIB )–7,245,SJIF–5,431 water molecules, metal ions, and co-crystallized ligands, which may interfere with the docking process or create artifacts. Hydrogen atoms were added to all polar residues tostabilize hydrogen bonding networks, and Kollman United Atom charges were applied. In addition, torsional flexibility was kept restricted on the protein side, assuming the receptor behaves as a rigid body during docking. The processed protein structure was saved in PDBQT format, which is compatible with AutoDock Vina. Prior to docking, the active site was visually inspected to confirm accessibility and thepresence of key bindingresidues. 2.2.LigandPreparation Twoligand molecules were selected for comparative docking: 1. Isoniazid –awell-established first-lineanti-tuberculosis drug usedas areference compound. 2. A novel compound – computationally designed and not yet synthesized, serving as a theoretical inhibitor. Both molecules were drawn in Avogadro molecular editor (version 1.2.0), and their geometries were optimized using the Universal Force Field (UFF) with the steepest descent algorithm. Optimization was conducted until the energy gradient converged below the threshold of 10⁻⁷ kcal/mol/Å. Following energy minimization, the ligands were saved in .mol and converted to.pdbformat using OpenBabel. In AutoDock Tools, rotatable bondswere detected and defined, Gasteiger charges were added, and torsion trees were generated. The final ligands were exported inPDBQT format, allowing flexibledocking around rotatable bonds. 2.3.Docking Procedure Molecular docking was performed using AutoDock Vina (version 1.1.2), a well-established open-source tool known for its speed and accuracy in predicting binding affinities. The docking grid box was defined to encompass t