Bioinformatic Application in Proteomic Research on Biomarker Discovery and Drug Target Validation

Wang, Ying; Chiu, Jen‐Fu; He, Qing-Yu

doi:10.2174/157489307779314294

Cited by 3 publications

(4 citation statements)

References 96 publications

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“…Ligand‐based drug design is the most effective and widely used method of drug development. This conventional method optimizes the structure and properties of the clinically approved drugs focusing on the basic scaffold and the second functional groups (Hassan Baig et al., ; Wang, Chiu & He, ). De novo drug designing also focuses on the designing of the new chemical compounds by modifying the parent drug compound.…”

Section: Computational Approaches To Drug Discoverymentioning

confidence: 99%

“…High‐throughput screening of small molecules includes screening strategies against huge libraries of chemical moieties on the basis of both structures of the drug target and chemical structure of the drug molecules. This method relies on the hit identification providing a rapid cost‐effective and time‐saving process of new and potent scaffolds (Hassan Baig et al., ; Miller et al., ; Wang et al., ).…”

Section: Computational Approaches To Drug Discoverymentioning

confidence: 99%

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Plasmodium falciparum: Multidrug resistance

Rout

Mahapatra

2019

Chem Biol Drug Des

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Malaria is the most lethal and debilitating disease caused by the protozoan parasite Plasmodium worldwide. The most severe forms of disease and the incidence rates of mortality are associated with P. falciparum infections. With the identification of disease source and symptoms, many chemical entities were developed naturally and synthetically for administration as a potential antimalarial drug. The major classes of approved antimalarial drugs that are governed as first‐line treatment in tropical and subtropical areas include quinolines, naphthoquinones, antifolates, 8‐aminoquinolines, and endoperoxides. However, the efficacy of antimalarial drugs has decreased due to ongoing multidrug resistance problem to current drugs. With increasing resistance to the current antimalarial artemisinin and its combination therapies, malaria prophylaxis has declined gradually. New‐generation antimalarial and novel drug target are required to check the incidence of malaria resistance. This review summarizes the emergence of multidrug resistance to known antimalarial and the development of new antimalarial to resolve drug resistance condition. Few essential proteins are also discussed that can be considered as novel drug target against malaria in future.

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Section: Computational Approaches To Drug Discoverymentioning

confidence: 99%

Section: Computational Approaches To Drug Discoverymentioning

confidence: 99%

Plasmodium falciparum: Multidrug resistance

Rout

Mahapatra

2019

Chem Biol Drug Des

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“…Bioinformatics software can use the three-dimensional structural information of the unliganded target to design entirely new lead compounds de-novo. This software allows rapidly and accurately docking large numbers of candidate molecules into the binding site of the target macromolecule prior to actual synthesis and biological studies [16]. Importance of bioinformatics and proteomics in identification of biomarker can be understood by (Figure 3) which define their role in detail.…”

Section: Biomarker In Drug Development and Bioinformaticsmentioning

confidence: 99%

Biomarkers: The Future of Medical Science to Detect Cancer

Karley¹

2011

J Mol Biomark Diagn

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The word biomarker in its medical context is a little over 30 years old, having first been used by Karpetsky, Humphrey, and Levy in the April 1977 edition of the Journal of the National Cancer Institute, where they reported that the "serum RNase level was not a biomarker either for the presence or extent of the plasma cell tumour. " Few new words can have proved so popular. A recent Pub-Med search lists more than 370,000 publications that use it! Part of this success can no doubt be attributed to the fact that the word gave a long -overdue name to a phenomenon that has been around at least since the seventh century B.C, when Sushustra, the " father of Ayurvedic surgery, "recorded that the urine of patients with diabetes attracted ants because of its sweetness. However, although the origins of biomarkers are indeed ancient, it is fair to point out that the pace of progress over the first 2500 years was somewhat less than frenetic [1]. More than 11 million people are diagnosed with cancer every year. It is estimated that there will be 16 million new cases every year by 2020 [2]. Cancer is a cluster of diseases involving alterations in the status and expression of multiple genes that confer a survival advantage and undiminished proliferative potential to somatic or germinal cells [3]. There is increasing evidence to suggest that cancer is also driven by 'epigenetic changes' like DNA methylation and altered patterns of histone modifications, leading to alterations in chromatin condensation status thereby regulating expression of certain set of specific genes [4]. Cancer cells display a broad spectrum of genetic alterations that include gene rearrangements, point mutations, and gene amplifications, leading to disturbances in molecular pathways regulating cell growth, survival, and metastasis. When such changes manifest in majority of patients with a specific type of tumour, these can be used as biomarkers for detection and developing targeted therapies, besides predicting responses to various treatments [5][6][7].

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“…Recent LC‐MS technological developments together with the integration of new analytical strategies significantly contributed to the acceleration of drug discovery and development (Lee and Kerns, ; Korfmacher, ). Furthermore, the development of specialized bioinformatic tools opened new opportunities for the identification and quantification of biomarkers (Palagi et al , ; Wang et al , ; Kumar and Mann, ). Undoubtedly, the meaning of bioanalysis evolved and motivated the continual development of LC‐MS‐based technologies and strategies (Chalkley, ; Honour, ).…”

Section: Introductionmentioning

confidence: 99%

Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry

Pailleux

Beaudry

2012

Biomedical Chromatography

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The development of LC-MS/MS instruments and related applications improved the large-scale analyses of proteins and peptides in complex biological mixtures. The historical factor limiting these types of studies was the lack of sensitivity and reproducibility. However, the capacity of these analyses to detect proteins and peptides was significantly enhanced to a point where they are routinely performed in specialized laboratories in support to drug development programs as well as prognostic and diagnostic investigations. The analytical strategy used in peptidomic analyses needs to minimize the fluctuation in data measurements that might mask or reduce the precision of the determinations and consequently reduce the sensitivity of the assay. Inherently, it outlines the importance of careful standardization to reduce technical and instrumental variation. Therefore, this review will focus on the strengths and the limitations of the different experimental approaches used for the integration of internal standards in peptidomic studies. This review will examine a wide variety of methods, reagents, instrumentations and data analysis tools available to design peptidomic experiments. Moreover, this review will focus on the importance of precision and accuracy in order to adequately establish analysis threshold to detect peptide expression differences.

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Bioinformatic Application in Proteomic Research on Biomarker Discovery and Drug Target Validation

Cited by 3 publications

References 96 publications

Plasmodium falciparum: Multidrug resistance

Plasmodium falciparum: Multidrug resistance

Biomarkers: The Future of Medical Science to Detect Cancer

Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry

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