Rational Design, Synthesis, and Biological Evaluation of Third Generation α-Noscapine Analogues as Potent Tubulin Binding Anti-Cancer Agents

Naresh Kumar Manchukonda,Pradeep Kumar Naik,Silja Joseph,Srinivas Kantevari,Manu Lopus,Seneha Santoshi,Balasubramanian Sridhar,Chandra Verma

doi:10.1371/journal.pone.0077970

Abstract

Systematic screening based on structural similarity of drugs such as colchicine and podophyllotoxin led to identification of noscapine, a microtubule-targeted agent that attenuates the dynamic instability of microtubules without affecting the total polymer mass of microtubules. We report a new generation of noscapine derivatives as potential tubulin binding anti-cancer agents. Molecular modeling experiments of these derivatives 5a, 6a-j yielded better docking score (-7.252 to -5.402 kCal/mol) than the parent compound, noscapine (-5.505 kCal/mol) and its existing derivatives (-5.563 to -6.412 kCal/mol). Free energy (ΔG bind) calculations based on the linear interaction energy (LIE) empirical equation utilizing Surface Generalized Born (SGB) continuum solvent model predicted the tubulin-binding affinities for the derivatives 5a, 6a-j (ranging from -4.923 to -6.189 kCal/mol). Compound 6f showed highest binding affinity to tubulin (-6.189 kCal/mol). The experimental evaluation of these compounds corroborated with theoretical studies. N-(3-brormobenzyl) noscapine (6f) binds tubulin with highest binding affinity (KD, 38 ± 4.0 µM), which is ~ 4.0 times higher than that of the parent compound, noscapine (KD, 144 ± 1.0 µM) and is also more potent than that of the first generation clinical candidate EM011, 9-bromonoscapine (KD, 54 ± 9.1 µM). All these compounds exhibited substantial cytotoxicity toward cancer cells, with IC50 values ranging from 6.7 µM to 72.9 µM; compound 6f showed prominent anti-cancer efficacy with IC50 values ranging from 6.7 µM to 26.9 µM in cancer cells of different tissues of origin. These compounds perturbed DNA synthesis, delayed the cell cycle progression at G2/M phase, and induced apoptotic cell death in cancer cells. Collectively, the study reported here identified potent, third generation noscapinoids as new anti-cancer agents.

Highlights

Unlike the current tubulin binding chemotherapeutic drugs such as Paclitaxel and Vinca alkaloids that are confounded by complications with undesirable side effects such as systemic toxicity, noscapine [1,2,3], an over-the-counter antitussive alkaloid [4,5], is endowed with better anti-cancer profile [6,7,8] and safer toxicity profile [9,10,11]
The initial structure of tubulin was obtained from the PDB database, the missing amino acids were filled based on homology model building and the protein structure was refined further using molecular dynamics (MD) simulation
The equilibration of the MD trajectories was monitored based on the convergence of plots of root-mean-square deviations (RMSDs) of Cα carbon atoms of tubulin during 10 ns of MD simulation starting from the initial structure (Figure 4A)

Summary

Introduction

Unlike the current tubulin binding chemotherapeutic drugs such as Paclitaxel and Vinca alkaloids that are confounded by complications with undesirable side effects such as systemic toxicity, noscapine [1,2,3], an over-the-counter antitussive alkaloid [4,5], is endowed with better anti-cancer profile [6,7,8] and safer toxicity profile [9,10,11]. Induces minor suppression of the dynamic instability of microtubules [13,14]. Noscapine has many advantages as a microtubule-binding agent [1].

Methods

Results

Conclusion