Original Article IDENTIFYING LEAD COMPOUNDS FOR POTENTIAL ANTI-TUBERCULOSIS DRUGS BY IN SILICO MYCOBACTERIUM TUBERCULOSIS SHIKIMATE KINASE INHIBITORS SELECTION OF CHEMICAL LIBRARY NUKI BAMBANG NUGROHO 1* , BELLA ETIKA 2 , SRI TEGUH RAHAYU 2 , AJI WIBOWO 1 , EKA SISKA 1 1 Research Center for Vaccine and Drug, National Agency for Research and Innovation (BRIN), Cibinong, West Java, Indonesia. 2 Pharmacy Study Program, Faculty of Health Sciences, Esa Unggul University, Jakarta-11510, Jakarta, Indonesia * Corresponding author: Nuki Bambang Nugroho; * Email: nuki001@brin.go.id Received: 24 Sep 2024, Revised and Accepted: 13 Jan 2025 ABSTRACT Objective: The present study aimed to identify Shikimate Kinase (SK) inhibitors as antitubercular agents from a chemical library by the utilization of molecular docking simulation, pharmacophore evaluation, and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) prediction approaches. Methods: A molecular docking study by Molecular Operating Environment (MOE) was used to screen 400,000 compounds from the Mcule ULTIMATE Express 1 chemical library. This docking study used a rigid docking technique to simulate the interaction between receptors and compounds. The screened compounds were then validated by pharmacophore and ADMET analyses to show the presence of positive characteristics. Results: The result of molecular docking simulation identified N-[2-(diethylamino)ethyl]-2-(pyrrolidin-1-yl)acetamide as the most promising candidate for targeting Mycobacterium tuberculosis Shikimate Kinase (MtSK), due to its binding energy score (-11.3412 kcal/mol) and suitability of interacting residues (Asp34 and Gly80). Moreover, this compound also shared similar pharmacophores with shikimate, and it had positive drug-like and ADMET properties. Conclusion: This work identified one candidate for SK inhibitor from a pool of five drug-like hit compounds. These inhibitors show promise as prospective candidates for the development of a new anti-tuberculosis therapy and warrant additional experimental investigation. Keywords: Mycobacterium tuberculosis, Shikimate pathway, Shikimate kinase, Molecular docking © 2025 The Authors. Published by Innovare Academic Sciences Pvt Ltd. This is an open access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/) DOI: https://dx.doi.org/10.22159/ijap.2025v17i2.52759 Journal homepage: https://innovareacademics.in/journals/index.php/ijap INTRODUCTION Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis (Mtb). Tuberculosis is transmitted by airborne transmission when patients infected with the disease expel saliva particles carrying the bacterium into the air, usually via coughing or sneezing. Presently, this disease remains a worldwide pandemic, leading to the demise of 1.3 million people out of around 10.6 million reported cases of tuberculosis in 2022. The data had risen in comparison to the preceding year, notably reaching 10.3 million in 2021, and 10 million in 2020 [1]. This emphasizes the need to rapidly treat this disease to protect humanity. Presently, tuberculosis still relies on the use of current therapies, which exhibit an estimated success rate of 85% in effectively healing people with tuberculosis. Untreated cases of tuberculosis are linked to a substantial death rate, estimated to exceed 50% [2]. As per the recommendations established by the World Health Organization (WHO), individuals diagnosed with drug-susceptible tuberculosis are recommended to follow a 6 mo treatment plan that includes the administration of isoniazid, rifampicin, ethambutol, and pyrazinamide [1]. In contrast, individuals with TB who do not show improvement after receiving one or more drugs would need alternate treatment strategies and maybe a longer length of therapy. Managing Extensively Drug- Resistant Tuberculosis (XDR-TB), which is unresponsive to rifampicin, any fluoroquinolone, and bedaquiline/linezolid, poses significant difficulties, and the prospects of achieving successful treatment outcomes are typically unfavorable [1, 3]. Enzyme-based drugs remain crucial in the process of screening and developing treatments due to their vital role in the life cycle and metabolism of pathogens [4]. Moreover, more than 50% of pharmacological compounds are intentionally engineered to interact with enzymes to produce the intended effects [5]. The shikimate (SKM) pathway has attracted attention as a promising target for the development of antimicrobial agents due to its exclusive presence in bacteria, particularly Mtb, fungi, and plants while being lacking in humans [6]. The SKM pathway plays a crucial role in the synthesis of vital substances, including ubiquinone, folic acid, aromatic amino acids, and other aromatic compounds. Therefore, this pathway has been recognized as a promising target for the development of drugs that may treat tuberculosis. SK is the fifth enzyme in the SKM pathway. The enzyme's function is to catalyze the conversion of SKM to Shikimate 3-Phosphate (S3P) by using ATP as a phosphate donor. The enzyme exists as a single unit with a molecular weight of 18.6 kDa and is composed of 176 amino acid residues [7, 8]. SK refers to a group of enzymes known as Monophosphate Nucleoside (NMPs) kinases. The enzymes consist of three components: the CORE, which has a loop that binds to phosphate; the LID, which contains amino acids that interact with ATP; and the NMP-binding domains, which are substituted by a site that binds to SKM. The LID domain has a flexible characteristic and plays a crucial role in the structural modifications that take place during substrate binding [9– 11]. The aroK gene encodes SK. Studies have shown that aroK is crucial for the survival of Mtb, and inhibiting the gene's function might result in the organism's death [12]. The SKM pathway utilizes erythrose-4-phosphate from the pentose phosphate pathway and phosphoenol pyruvate from the glycolysis pathway as starting materials to synthesize chorismic acid through a series of seven enzymatic reactions. The three-dimensional structure of the seven enzymes involved in the SKM pathway of Mtb has been determined [8, 13]. While the importance of the SKM pathway has been confirmed, only 3-Dehydroquinate (DHQ) synthase, SK, and chorismate synthase have been individually validated [8]. Among these three enzymes, only SK has been used for computer-based screening of anti-TB agents [14–16]. Due to its more complete data compared to other targets, it would be more feasible to develop a screening system for anti-TB agents based on SK. International Journal of Applied Pharmaceutics ISSN- 0975-7058 Vol 17, Issue 2, 2025