IN SILICO IDENTIFICATION 0F PUTATIVE DRUG TARGETS IN STAPHYLOCOCCUS AUREUS


IN SILICO IDENTIFICATION 0F PUTATIVE DRUG TARGETS IN STAPHYLOCOCCUS AUREUS  

ABSTRACT

Staphylococcus aureus is one of the most important and studies gram positive bacterial strains, which have a great potential to infect human being as well as other mammals. Staphylococcus aureus is a major cause of infections responsible for much life threatening diseases like toxic-shock syndrome, staphylococcal scarlet fever, meningitis, osteomyelitis etc. infection due to these strains are difficult to treat. This research work focused on the identification of drug target enzymes in staphylococcus aureus. These drug target enzymes development of the new antibiotic which can kill or suppress the growth of pathogen with no effect in the host. The E-value threshold cut-off was set to 0.001.

TABLE OF CONTENTS

Title page i

Certification ii

Dedication iii

Acknowledgement iv

Abstract v

Table of content vi

CHAPTER ONE 

Introduction 

CHAPTER TWO 

Material and methods 

CHAPTER THREE

Result 

CHAPTER FOUR 

Discussion 

CHAPTER FIVE 

Conclusion 

References 

CHAPTER ONE

INTRODUCTION 

Staphylococcus aureus a member of staphylococcaceae is considered as an opportunistic pathogen for the different mammals including livestock as well as humans (Lowy1998, projan and novick, 1995). It has been reported that staphylococcus aureus is resistance against varies antibiotics present in the market (Lowy, 1998; walsh and bowe, 2002). this bacterial strain word widely known for causing many of the severe and deadly disease like osteomyelitis bacteremia , endocarditic, meningitis, scalded skin syndrome, toxic shock syndrome, food poisoning, etc( Lowy, 1998; drekema et al ., 2001 ). It is the primary cause of lower respiratory tract infections surgical site infection (Richard, et al., 1993) and the second leading of nosocomial  bacteremia (wisplinghoff et al ., 2004) pneumonia, and cardiovascular infections (Richard et al., 1993). Beside these disease, it is also found on the skin of the human beings and causing major problems like pimples, sour throat, hair follicle infection, acne, and sties (a sty is an inflammation of a gland in the eyelid). It is also causes boils, which are deeper pus-filled abscesses of the skin and underlying tissue (freeman-cook and freeman-cook, 2006 Carleton et al., 2004; king et al., 2006). In common with other facultative aerobes, staphylococcus aureus can grow in the absence of oxygen either by fermentation or by using an alternative terminal electron acceptor, such as nitrate.

    Various studies suggest that oxygen play a role in the pathogenesis of staphylococcus aureus, in both is capacity to produce virulence factors and its ability to persist and grow in different and often hostile environment niches (Chan and foster, in 1998; clement and foster, ohisen et al., 1997; Ross and onderdonk, 2000). The bacteria contain or can produce a variety virulence factor like adhesion, colonization, exoenzyme and exotoxins, capsule etc.These virulence factors help the bacteria to attack to the host cell, it can bind to protein such as fibronectin, laminin, vitronectin, and collagen, which form the extra cellular matrix of epithelia and endothelia surfaces (Gillaspy et al., 1990; freeman-cook, 2006). The resistance to antibiotics emerged and spread rapidly among strains of staphylococcus aureus, about 90% of staphylococcus aureus strains are currently resistant to penicillin and derivatives. To combat this problem, new derivatives of penicillin were introduced (Lowry, 2003; freeman-cook, 2006).

    Today, around 50% of all staphylococcus infections are multidrug resistant (resistant to penicillin, methicillin, tetracycline, and erythromycin). One antibiotic stood for years as a drug that did not cause resistant bacteria to emerge. It often thought of as “last resort “, the name implies exactly how it has been used. Thus, the battle between human and bacteria continues (Freeman- cook et al., 2006). The computational approach has been use to investigate novel drug targets in other pathogenic organisms such as pseudomonas aeruginosa (sakharkar et al., 2004; perumal et al., 2007) and in helicobacter pylori (outla et al., 2006). As most currently known, antibacterial are essentially inhibitors of certain bacterial enzymes. In this study, we have adopted a strategy for comparative pathway analysis to find out some potential target against staphylococcus aureus. Only those enzymes which show unique properties than the host were selected as the target.

         Staphylococcus aureus is a vanguard for both nosocomial and community- acquired infection. It is the primary cause of surgical infection and lower respiratory tract infections, (Richard et al., 1993) and the second leading cause of cardiovascular infections, and pneumonia (Richards et al., 1999). Because of evolved resistance to antimicrobial drugs such as penicillin newer narrow-spectrum β-lactamase-resistant penicillin antimicrobial drugs (e.g. methicillin, oxacillin) infection with staphylococcus aureus are especially difficult to treat and this resistance appeared soon after they were introduced into clinical practice respectively in 1940s and 1960s (Lowy et al., 2003 ). Initially resistance to penicillin was restrained to small number of hospitalized patients, but as use of penicillin increased, resistance spread first to other hospitals and then into the community (chambers at el., 2001). Greater than 80% of community and hospital- acquired staphylococcus aureus isolated were resistant to penicillin by the late 1960s (Lowy et al., 2003). Current report suggests that the spread and evolution of methicillin-resistant staphylococcus aureus (MRSA) seems be following identical wavelike emergence pattern (Chamber et al., 2001). In many US hospitals, MRSA is now endemic and epidemic along term care facilities and communities (Straus Baugh et al., 1960). National nosomial infections surveillance system's data suggest that the proportion of staphylococcus aureus isolate that are resistant to methicillin has increased to 59.5%-64.4%, in intensive care unit (klevens et al ., 2006). Accurate national estimate of incidence are needed for understanding the magnitude of the problem. Nevertheless, national studies examine the effect of staphylococcus aureus or MRSA on the healthcare system are greater than 5years old (Kuehnert et al., 2005). Noskin et al., estimated that there were 290,000 staphylococcus aureus related hospitalization for 1999-2000 and reported that125, 969 (43.2%) were likely resistant to methicillin (Kuehnert et al., 2005). The infections caused by this pathogen range from mild infections such as skin infections, poisoning to life threatening infections such as pneumonia, sepsis, osteomyelitis and infection endocarditic. Methicillin- resistant staphylococcus aureus is considered as super bug which was first reported in 1961 and now-a-days cause mortality rate of 39% while MRSA cause 24% death [laupland et al .., 2008].

 The currently known targets of staphylococcus aureus include PBP (penicillin binding protein) of peptidoglycan biosynthesis pathway. Previously, beta-lactam antibiotics were knows to be effective against them, but due to production of altered form of PBP protein as well as beta-lactamase enzyme synthesis those drugs are not effective now, hence, our current study involves identifying targets apart from PBP(Hao et al., 2012). Another antibiotics prescribed is fluroquinolone. Fluroquinolone target DNA Gyrase A enzyme-essential for the replication, supercoiling of DNA. But according to Stephen et al., a highly signification associate between levofloxaxin and ciprofloxacin treatment and subsequent isolation of MRSA is reported (Weber et al., 2003). Linezolid, a new class of antibiotic called oxazolidinones is used to treat MRSA, which involve the mechanism of binding to bacterial 23s ribosomal RNA but  of the 50s subunit and thus inhibiting the formation of functional 70s initiation complex but between April 13 and June 26 ,2008,12 patient were identified by LRSA (linezolid resistant staphylococcus aureus). All the isolates were detected with a point mutation in 23s RNA. It was concluded that the clinical outbreak of LRSA medicated by the (Fr gene was related with extensive usage of linezolid (Tsiodras et al., 2001).   In this study, we have tried to search for some potential therapeutic targets other than the target discussed above. We have implemented an approach considering two pathogen in the senses that it must be associated with replication as well as viability of the pathogen. Secondly, the target should not be homologous to human. The non homologous property of these proteins helps to establish highly selective drug against the pathogen preventing the possibility of the cross reaction.

With the human host this may help to minimize the side effect of the proposed drug (skaharkar et al.,2001). By this approach, we have found some targets which are not only essential and non-homolog but also bypass the resistant mechanism of existing targets and some targets are involved in the metabolic pathway of pathogen of which is not exploited as potential target area (Nathan et al ., 2004). We have also identified the membrane-bound essential, non-human homolog proteins emphasizing the fact  that 60% of the drug target is membrane-bound (arinaminpathy et al., 2009). 

            Staphylococcus aureus is an important pathogen causing a wide range of infection in the hospital and community setting. In order have adequate information for treatment of staphylococcus aureus infections, it is crucial to understand the trend in the antibiotic-resistance patterns. In addition, the occurrence and changes in types of staphylococcus aureus, colonial identities, and their geographic spread is essential for the establishment of adequate infection control programmes. In this study, 68 staphylococcus aureus isolates obtained from clinical and non-clinical sources Nigeria  between January and April 2009 were characterized using phenotype and molecular method.

              Staphylococcus areus can exemplify better than any other human pathogen the adaptive evolution of bacteria in the antibiotic era, as it has demonstrated a unique ability to quickly respond to each new antibiotic with the development of a resistant mechanism, starting with penicillin and methicillin, until the most recent linezolid and daptomycin. Resistant mechanism included inactivation of the antibiotic (penicillinase and aminogylcoside-modification enzymes) alteration of the target with decrease affinity for the antibiotic notable example being penicillin-binding protein 29 of methicillin-resistant Staphylococcus aureus and D-ala-D-lac of peptidoglycan precursors of Vancomycin-resistant strains]and afflux pumps [fluroquinolone and tetracycline].Complex genetic arrays[Staphylococcus chromosomal cassette mechanism elements or the Van A Operonl have been acquired by Staphylococcus aureus through horizontal gene transfer, while  resistance to other antibiotics, including some of the most recent ones [e.g fluroquinolones linezolid and daptomycin have developed through spontaneous mutations and positive selection. Detection of the resistance mechanisms and their genetic basis is an important support antibiotics susceptibility and surveillance in Staphylococcus aureus.

    The need for new drugs comes from the widespread resistance to those in current use. New drugs targets are required to allow the discovery of chemically diverse effective drugs. The search for such new targets and new drug chemo types will likely be helped by the advent of functional genomics and structure-based drug design. After validation of the putative targets as those capable of providing effective and safe drugs, targets can be used as the basis for screening compounds in order to identify new leads, which in turn, will qualify for lead optimization work. Many enzyme in macromolecular and metabolite synthesis are promising potential targets, some of which have been established in many micro organisms.

     Any gene necessary for the viability of a pathogenic organism may be a possible drug target, particularly when the sequence of that gene has little or no similarity to those of the host and the pathogen can be effectively used for designing a drug specifically targeting the pathogen. Detection of bacterial genes that are non-homologous to human genes and are essential for the survival of the pathogen represents a promising means of identifying novel drug targets (sakharkar et al.,2004).

  The computation approach has been used to investigate novel drug targets in other pathogenic organisms such as pseudomonas aeruginosa (sakharkar et al., 2004; perumal et al., 2007) and in Helicobacter pylori (dutta et al., 2006). In their study, the search for potential vaccine and drug targets against staphylococcus aureus was carried out by in silico.

AIM AN OBJECTIVES 

AIM

To identify different drug target enzymes in staphylococcus aureus.

PRIMARY OBJECTIVES

1. To extract protein from NCBI( national center for biotechnology information) database in staphylococcus aureus.

2. To identify non-human homolog proteins to serve as drug target.

3. To find and locate those essential genes of staphylococcus aureus that play important roles in the normal functioning of the bacterium with the host and to short list them in the view of drug targeting.

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IN SILICO IDENTIFICATION 0F PUTATIVE DRUG TARGETS IN STAPHYLOCOCCUS AUREUS



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