15-07-2014, 02:40 PM
Background
ABSTRACT
Background: Cancer is the largest cause of death among people in all over world. It has also been proved from the earlier study that DNA repair help in disease treatment. DNA damage is a most important cause of the cancer. This DNA damage is repaired by alkylat-ing agents. Recent studies have added the importance of some proteins like AlkB protein, which play an active role in the DNA damaging drug, and cancer treatment. Therefore, in present study we are indented to design various analogs through various Bioinformatics tool and software.
Material and method: Docking was done with iGEMDOCK to predict the lowest ener-gy compound. Interaction energy and their validated structure are predict by the using of post docking analysis. Designing analogs was done with the Chemsketch software, used to draw chemical structure of any compound. Openbabel was used to convert different file formats from one to other. Protein structures for docking study were collected from protein model databases with the PMDB Ids PM0076294 and PM0076284 for hABH1 and hABH4 respectively.
Results and discussion: The result of lead compounds PM0076294-ZINC_14644239-1.pdb and PM0076284-ZINC_3874317-1 showed best interaction energy with hABH 1 and 4 respectively. Protein-complex-compound interaction energy of the best lead compound was -110.17 and -118.115. Based on the Interaction energy shown by the best lead compound, four analogs were designed. The protein interaction energy was calculated for the four designed analogs and lead compound were predicted in the interaction energy table.
Conclusion: Docking study hABH1 and 4 and design analogs was performed. Their de-sign analogs and inhibitors are useful for the chemotherapy and anti cancer drug design.
Keyword: Inhibitor, Analogs, iGEMDOCK, Chemsketch
1. Introduction
Combination of biochemistry and bioinformatics analysis led to the discovery of oxida-tive demethylation, a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein (Kurowaski et al., 2003). Escherichia coli, in particular on the adaptive (Ada) response, which involves the upregulation of four genes: ada, aidB, alkA and alkB (Sedgwick et al., 2007). The Ada protein is a multifunctional DNA methyltransferase that also acts as a transcriptional activator of the response. The exact function of AidB, a fla-vin-binding protein, remains to be explained and AlkA is a DNA glycosylase with a broad specificity.
AlkB catalyses the demethylation of 1-methyladenine and 3-methylcytosine in DNA and RNA, coupled to the decarboxylation of 2-oxoglutarate (2OG) to succinate and CO2 (Falnes et al, 2002; Trewick et al, 2002). Homologues of AlkB have been identified in species ranging from bacteria to humans; eight human homologues (ABH) have been de-scribed, but only two, ABH2 and ABH3, are known to repair.
Numerous AlkB homologues are found in viruses, bacteria and eukaryotes, including eight human homologues (hABH1-8) (Helleday et al., 2008). AlkB is one of four proteins involved in the adaptive response to DNA alkylation damage in Escherichia coli and is highly conserved from bacteria to humans (Welford et al., 2003). Alkylating agents are employed as antiviral drugs and are used in chemotherapeutic treatment of cancers (Frankfurt et al. 1991).
Alkylating agents are ubiquitous. They are generated endogenously during the metabol-ism, and are found in the air, water and foods, although generally in low concentrations.
Biological name of hABH1 protein is Alpha-ketoglutarate-dependent dioxygenase AlkB1. They protein are localized in Mitochondrion. Nucleus mainly localizes in euch-romatin, largely excluded from heterochromatin and nucleoli.
They are belongs to the AlkB families. hABH1 is use for DNA repair, DNA damage, RNA repair. They are the some biological function of hABH1 dioxygenase that repairs alkylated single-stranded DNA and RNA containing 3-methylcytosine by oxidative de-methylation. Further study of human AlkB homologues initiates with the need for infor-mation of structural conformation of these molecules, which can be potential targets for designing inhibitors for cancer therapy (Shankaracharya et al.2011).
Recently in 2007 function of hABH4 has been investigated by Bjørnstad. He tested the enzymatic activity of hABH4 towards 5-methylcytosine in vitro and in vivo. Two pro-teins identified as interactants of hABH4 by the Yeast Two-Hybrid method, may indicate a role of hABH4 transcriptional regulation (Bjornstad 2007).
Alkylating compounds are ubiquitous and modify cellular macromolecules such as DNA and RNA. Human homologues of the Escherichia coli DNA repair enzyme AlkB are termed ALKBH enzymes. Some ALKBH enzymes have been demonstrated to function as nucleic acid demethylases, catalyzing the oxidative demethylation of 1-methyladenine and 3methylcytosine in DNA and RNA [Aravind L et al.2001]. One such mechanism in-volves the E. coli AlkB protein (EcAlkB), which directly reverses alkylations at the N1-position of purines and the N3-position of pyrimidines, for example, 1-methyladenine (m1A) and 3-methylcytosine (m3C); the first EcAlkB substrates identified. EcAlkB be-longs to the superfamily of iron(II)- and 2-oxoglutarate (2OG) dependent dioxygenases .
The crystal structures of AlkB, hABH2, and hABH3 have been solved (Sundheimet al., 2006; Yang et al., 2008; Yu et al., 2006) and a common double strand β-sheet core with fundamental changes in the oligonucleotide binding regions(Simmons et al., 2008) has been revealed. Several drugs in cancer chemotherapy work by producing excessive DNA damage in tumor cells leading to cell death directly or following DNA replication (Helle-day et al., 2008).
1 hABH1 and hABH4 used for the cancer treatment:-
Environmental causes of cancer, such as cigarette smoke, ionizing radiation, sunlight, aflatoxin and certain viral infections are well documented; however, individuals who avoid exposure to these agents remain susceptible to cancer.
Reduced DNA repair activity causes certain types of cancer and may be involved in ag-ing. Inhibition of DNA repair mechanism through alkylating agents in tumor cells is an important method for cancer treatment. All cancer cells carry mutations in genes involved in growth control, and most are genetically unstable.
DNA damage through alkylating agents is one of the important weapons for selective killing of Cancer cells. E. coli AlkB and its human homologue are recently discovered as alkylating agents involve in oxidative demethylation of 1-methyladenine and 3-methylcytosine, which has expanded the concept of alkyla¬tion repair, by direct reversal method.
Alkylating agents exists everywhere; they are generated during metabolism and found in air, water and foods, though at low concentrations (Drabløs F et al. 2004).Further study of human AlkB homologues initiates with the need for information of structural confor-mation of these molecules, which can be potential targets for designing inhibitors for cancer therapy. They alkylating agent are use for the anti cancer-drugs like.
Literature review
To address the need to provide a more detail and rapid analysis of medical task, risk as-sessment tool and their various inhibitors have been widely investigated. H. Kataoka and colleagues shown that alkB mutants had increased sensitivity towards the SN2-type me-thylating agent MMS, and experiments based on the survival of alkylated phage in wild-type cells and alkB mutant cells indicated that it was involved in DNA repair discovered( Kataoka et al.,1983). AlkB is an opportunistic protein that is able to take on different roles. It also indicates that repair mechanisms are dynamic, where enzymes may be re-cruited into new roles as part of the adaption process to new challenges. Alkylation resis-tance was an intrinsic property of AlkB itself, as the expression of E. coli AlkB in human cell lines gave the same alkylation-resistant phenotype as in E. coli. Shortly after this the first human AlkB homologue was identified (Wei et al., 1996). AlkB specificity is limited to the N1 position of purines and N3 of pyrimidines (Begley et al., 2003) AlkB mystery solved oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct reversal, which is in contrast to DNA glycosylases that remove lesions on the N3 position of purines and less frequently the O2 position of pyrimidines (Sedgwick et al., 2002). Greater insight into DNA binding and substrate base recognition comes from a comparison of the AlkB-ssDNA complex with the AlkB holoenzyme structure. In the absence of bound substrate, residue Y76 in the active site cleft adopts a confirmation that is flipped away from the active site providing open access for an incoming base (Holland et al., 2010). The E. coli protein AlkB was recently shown to be an oxidative DNA demethylase that repairs the cytotoxic lesions 1-meA and 3-meC in DNA. AlkB homologues could be involved in RNA processing as it was found in RNA viruses (Falnes et al., 2002). The human genome sequence has already markedly influenced the field of DNA repair.
Many of the genes listed were discovered as investigators searched the expanding data-base for sequence similarity to genes discovered in model organisms (Wood et al., 1999). Falnes,P.O. and Rognes,T. (2003) previously generated a limited sequence phylogeny of bacterial AlkB proteins, based on _60 protein sequences retrieved by PSI-BLAST
Inhibitors
AlkB is inhibited by high concentrations of 2OG, analogues of 2OG, including 2- mer captoglutarate, were found to specifically inhibit AlkB. The flavonoid quercetin inhibits both AlkB and the 2OG oxygenase factor inhibiting hypoxia-inducible factor (FIH) in vitro. The inhibition of AlkB by quercetin is, predominantly, due to non-specific iron chelation. Quercetin is a good iron chelator and its regulatory role could in part be due to its effect on iron concentrations and consequently the activity of the Fe (II) dioxygenas.
Conclusion
In the medical science, cancer is a broad group of various diseases. Typically, these are study in clinical trials to compare the proposed treatment to the best existing treatment. They may be entirely new treatments, or they may be treatments have been used success-fully in one type of cancer, and are now being tested to see whether they are effective in another type. hABH1 and 4 will initiate the research on identifying a suitable mechanism of repair of alkylation damaged DNA and thus, provide better control on cancer treatment as these DNA repair systems are essential for the maintenance of genome integrity. Consequently, the deregulation of repair genes can be expect to associate with significant, detrimental health effects, which can include an increased prevalence of birth defects, an enhancement of cancer risk, and an accelerated rate of aging.
Docking study of hABH 1 and 4 has show the significant improvement in the prediction problem, particularly in the diagnosis of disease. This study demonstrated active site by docking and design analogs, which further confirm performance of this study successful and theyhelp to improve the anticancer us drug designing.