QSAR Regression Models for Predicting the Activity of Inhibitors of Staphylococcus Epidermidis

QSAR Regression Models for Predicting the Activity of Inhibitors of Staphylococcus Epidermidis

Sharav A. Desai
DOI: 10.4018/IJQSPR.313712
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Abstract

Staphylococcus epidermidis is a common symbiont bacteria, and these are common causes of nosocomial infections. The QSAR model for the identification of inhibitors against Staphylococcus epidermidis is developed. A database of around 600 compounds with known inhibitory zone values was collected. Descriptors representing structural and functional properties were calculated using Alvadesc v.1.02. This database was curated using feature selection and extraction procedures. The model was developed using four different machine learning algorithms on a training set called multiple linear regression, support vector regression, random forest regression, and random tree regression. The model performance has been assessed by traditional metrics including Pearson's correlation coefficient, coefficient of determination, mean absolute error, and root mean square deviation. The author also has performed external validation, cross-validation, and y-randomization test. Models with reasonably good performance were built and can be used for the virtual screening of inhibitors.
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Introduction

Staphylococcus epidermidis is a coagulase-negative gram-positive bacterial that most commonly lives on the human skin. They are known to be the most common cause of nosocomial infection and they travel into the human body through the implantation of prosthetic devices(Lax & Gilbert, 2015; Zheng, Ma, Zhang, Li, & Zhang, 2018). Patients with prosthetic devices like valves, central lines, cardiac devices, catheters, and patients under IV infusion are at greater risk of getting infected with Staphylococcus epidermidis (Cheung & Otto, 2010). These organisms are known to survive in the human body by forming a biofilm, which prevents them from the actions of the immune system(Otto, 2009). If this infection is not treated then it can result in sepsis or septic shock which do have high mortality(G. Kumar et al., 2011). In a coagulase-negative gram-positive related infection, complete removal of the infected prosthetic device and prolonged antibiotic therapy is required. Bloodstream Infections related to the catheter are estimated to reach 250,000 cases per year in the U.S with a mortality rate of 1-25%. Antibiotic resistance is another problem that is nowadays growing into this strain. The stains are found to be developed resistance to methicillin, the first choice of antibiotic against this infection(Diekema et al., 2001). Apart from methicillin this strain also acquired resistance against rifamycin, fluoroquinolones, gentamycin, tetracyclines, chloramphenicol, erythromycin, clindamycin, and sulphonamides(Rogers, Fey, & Rupp, 2009). Currently, it is also understood that S. epidermidis produces phenol soluble modules which can kill both red and white blood cells. S. epidermidis also plays a reservoir role to reserve genes, which can play a role in antibiotic resistance in S. aureus after horizontal gene transfer(Cheung et al., 2010). The epidemiology and transmission of infection are also poorly understood, even though the strain is known to cause the nosocomial infection past 30 years(Archer, 1988). The significance of infection through S. epidermidis also increases as the emergence of livestock-associated infections is also being subject to investigation(Cuny et al., 2017). S. epidermidis is believed to be innocuous in contrast to its cousin S. aureus(Foster, 2005). Some sporadic occurrences of toxic shock syndrome and enterotoxin in coagulates negative strain including S. epidermidis are also reported(Bautista, Gaya, Medina, & Nunez, 1988; Marin, de La Rosa, & Cornejo, 1992). S. epidermidis secret several proteins/enzymes which are known to involve into destruction of host tissues. Many of them are from the protease group, which also contributes to virulence. S. epidermis is also known to detoxify fatty acids which are harmful to the bacteria by secreting fatty acid modifying enzymes(Chamberlain & Brueggemann, 1997). The type and severity of the infection decide the treatment. Systemic infection patients require parenteral therapy and 80% of the strains are known to have methicillin resistance in such cases. The duration of the therapy depends on the clinical presentation of the condition.

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