GA-SMLR-Based QSAR Modeling and Molecular Docking Studies of Bisamidine Derivatives as NMT Inhibitors

GA-SMLR-Based QSAR Modeling and Molecular Docking Studies of Bisamidine Derivatives as NMT Inhibitors

Sapna Jain Dabade, Dheeraj Mandloi, Amritlal V. Bajaj, Naveen Dhingra
DOI: 10.4018/IJQSPR.2020100101
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Abstract

The present investigation deals with a combination of genetic algorithm-stepwise multiple linear regression (GA-SMLR)-based QSAR modeling and molecular docking applied to bisamidine analogues in an attempt to explore their role as novel NMT inhibitors of Candida albicans. In this regard, 43 bisamidine analogues were investigated for the development of mathematical models. The robustness of the proposed QSAR model was not only ascertained through traditionally used internal and external validation statistical parameters (Q2= 0.740, R2 = 0.819, R_Pred^2 = 0.636) but also through various R_(m)^2 metrics proposed by Roy and Mitra. The descriptors recognized in the QSAR analysis have culminated a significant role of atomic van der Waals volume, topology, nature of bond and dipole moment to modulate the antifungal activity of compounds under investigation. The most active compound revealed enhanced binding potency with MolDock score of -183.451 kcal/mol and displayed hydrogen bond interactions with active amino acids Leu177, Thr211, Tyr225, and IIe111 of NMT.
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Introduction

Systemic fungal infections can be life-threatening and may turn out to be the major reason of morbidity and mortality (Brown et al., 2012). It has been shown that Candida and Aspergillus are the most common fungal pathogens, specifically among patients with compromised immune function (Richardson, 2005; Garbino et al., 2002; Hobson, 2003). Even after significant progress in antifungal drug development, currently available three main classes of antifungal drugs namely polyenes, azoles and echanocandins suffer from the problems like limited antifungal spectrum, poor efficacy, renal toxicity, drug interactions and resistance (Dismukes, 2000; Chang et al., 2017; Chen & Sorrell, 2007; Lai et al., 2008; Vandeputte, Ferrari & Alix, 2012) . Fungal infections pose a great threat and global economic burden (Hoffman et al., 2005; Daele, 2019). In this context, research on new classes of potent antifungal drugs and targets is an urgent need for scientific society (Sangamwar, Deshpande, & Pekamwar, 2008; Sheng & Zhang, 2011; Ngo, Garneau, & Green 2016; Mazu, 2016).

Candida albicans is the principal cause of systematic fungal infections in immuno-compromised persons (Andes, 2012). Genetic and biochemical studies have revealed that enzyme myristoylCoA:protein N-myristoyltransferase (NMT) plays crucial role to sustain the viability of Candida albicans. In this line of action, NMT seems to be an emerging target for antifungal drugs (Devadas et al., 1997; Bhatnagar et al., 1999; Prasad, Toraskar, & Kadam, 2008).

Bisamidine derivatives have been screened as anti-bacterial, anti-cancer and anti- inflammatory drug candidates, thereby attracting the interest of researchers (Panchal et al., 2009; Butler et al., 2010; Arya, Kumar, Roy, & Sondhi, 2013). Recent studies have shown their potential for antifungal activity against a diverse panel of pathogenic fungi with unique mechanism of action to kill fungi by binding and inhibiting DNA replication as well as RNA synthesis (Nguyen, 2015).

Traditionally, drugs were discovered by synthesizing compounds which is an expensive, challenging, lengthy and interdisciplinary approach. Pharmaceutical industry is striving for ways to improve the efficacy of drug discovery process. To combat, accelerate and economize these problems, structure and ligand based drug design have emerged as revolutionary tools in recent years (Tang et al., 2006; Jorgensen, 2009; Yang et al., 2012; Roy, 2019) .

Researchers have been successfully using these computer aided tools to investigate new drug candidates that are highly potent for the antifungal activity. QSAR (Quantitative Structure-Activity Relationship), one of the ligand-based modeling tools has helped researchers in stretching a large library of possible drug candidates for selectivity and potency (Cronin, 2010;Roy, Kar, & Das, 2015). QSAR relies on generation of virtual models so as to explore dependence of physico-chemical activities with chemical structure of the concerned compound (Topliss, 1993; Selassie, 2003). Additionally, the structure-based drug designing approach, “molecular docking”, is a highly useful technique to explore the most active region of protein where the ligand–receptor interaction becomes prominent (Ferreira, 2015; Lounnas et al., 2013).

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