Research Article: Computational, crystallographic studies, cytotoxicity and anti-tubercular activity of substituted 7-methoxy-indolizine analogues

Date Published: June 4, 2019

Publisher: Public Library of Science

Author(s): Katharigatta Narayanaswamy Venugopala, Sandeep Chandrashekharappa, Melendhran Pillay, Hassan H. Abdallah, Fawzi M. Mahomoodally, Subhrajyoti Bhandary, Deepak Chopra, Mahesh Attimarad, Bandar E. Aldhubiab, Anroop B. Nair, Nagaraja Sreeharsha, Mohamed A. Morsy, Shinu Pottathil, Rashmi Venugopala, Bharti Odhav, Koleka Mlisana, Mohammad Shahid.


Indolizines are heteroaromatic compounds, and their synthetic analogues have reportedly showed promising pharmacological properties. In this study, a series of synthetic 7-methoxy-indolizine derivatives were synthesised, characterised and evaluated for in vitro whole-cell anti-tuberculosis (TB) screening against susceptible (H37Rv) and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) using the resazurin microplate assay method. The cytotoxicity was evaluated using the MTT assay. In silico molecular-docking study was conducted for compounds 5a-j against enoyl-[acyl-carrier] protein reductase, a key enzyme of the type II fatty acid synthesis that has attracted much interest for the development of novel anti-TB compounds. Thereafter, molecular dynamic (MD) simulation was undertaken for the most active inhibitors. Compounds 5i and 5j with the methoxy functional group at the meta position of the benzoyl group, which was at the third position of the indolizine nucleus, demonstrated encouraging anti-TB activity against MDR strains of MTB at 16 μg/mL. In silico studies showed binding affinity within the range of 7.07–8.57 kcal/mol, with 5i showing the highest binding affinity. Hydrogen bonding, π-π- interactions, and electrostatic interactions were common with the active site. Most of these interactions occurred with the catalytic amino acids (Pro193, Tyr158, Phe149, and Lys165). MD simulation showed that 5j possessed the highest binding affinity toward the enzyme, according to the two calculation methods (MM/PBSA and MM/GBSA). The single-crystal X-ray studies of compounds 5c and 5d revealed that the molecular arrangements in these two structures were mostly guided by C-H···O hydrogen-bonded dimeric motifs and C-H···N hydrogen bonds, while various secondary interactions (such as π···π and C-H···F) also contributed to crystal formation. Compounds 5a, 5c, 5i, and 5j exhibited no toxicity up to 500 μg/mL. In conclusion, 5i and 5j are promising anti-TB compounds that have shown high affinity based on docking and MD simulation results.

Partial Text

Mycobacterium tuberculosis (MTB) is the bacterial pathogen that underlies the infectious disease known as tuberculosis (TB). This disease affects the lungs and a number of other body systems and structures. According to WHO 2018 report, TB resulted in nearly 1.3 million deaths in those who are HIV-negative, and in 300,000 deaths among those who are HIV-positive [1]. Every year, new TB cases are reported worldwide and human immunodeficiency virus (HIV)-infected persons are up to 37 times more vulnerable to developing TB [2]. The development of multi-drug-resistant (MDR)-TB, extensively drug-resistant (XDR)-TB, and totally drug-resistant (TDR)-TB [3], as well as co-infections with acquired immunodeficiency syndrome (AIDS) and the risks involved in cases of TB among patients with diabetes mellitus [4], has resulted in a grave situation worldwide. Treating MDR-TB and XDR-TB is difficult, as second-line drugs have become far less effective [5]. This problem has been made worse by the evolution of TDR MTB strains [6] that are untreatable using the existing arsenal of anti-TB drugs. Based on the last 40 years of academic and pharmaceutical industry inventions, only bedaquiline (1) was the first novel anti-TB drug permitted by the United States Food and Drug Administration (US FDA) authority in December 2012 for the treatment of MDR-TB [7], while delamanid (2) was the second anti-TB agent to be approved by the European Medicines Agency (EMA) in late 2013 [8] (Fig 1).

Indolizine compounds were previously identified as a class of anti-TB agents against MDR strains of MTB. Here, we presented our medicinal chemistry efforts that were aimed at screening indolizine analogues with various functional groups to determine their anti-TB activity in vitro. We performed computational docking for the compounds 5a to 5j and dynamics simulations for the compounds 5i and 5j, and we also detailed the crystallographic insights of two selected compounds that had different substituents to assess the role of inter- and intra-molecular interactions. Compounds 5i and 5j emerged as promising anti-TB agents against MDR strains of MTB with no toxicity up to 500μg/mL. Docking and MD-simulation results tended to support the corresponding observed biological activity; these data showed that 5j has higher binding affinity when compared with 5i. The findings of the crystallographic analysis clearly suggest that the molecular arrangements of the 5c and 5d structures are mostly guided by C-H···O hydrogen-bonded dimeric motifs and C-H···N hydrogen bonds, while various secondary interactions (including π···π and C-H···F) were also found to contribute to the crystal formation.