Protein and Peptide Letters - Volume 16, Issue 5, 2009

This special hot-topic issue focuses on 3 “P” words - Proteome, Protein and Peptide, in this fast-discovering field of molecular medicine. Indeed, the volume of indexed publications and relevant successfully filed patents could reflect the importance of the “3Ps” in this topic (see Table 1). The major scope herein is to highlight some novel and innovative molecular and cellular approaches in these “3Ps” for identification of disease biomarkers as diagnostics and development of potential biological therapeutics for the treatment of diseases like cancer and immunological disorders. In the year 2000, the completion of human genome sequence has brought forth a new set of challenges for advancing science and technology. In particular, the emergence of genomics, proteomics, and bioinformatics has allowed us to systematically analyze large amount of sequence information and expression profiling data and studying biological systems on a global level. In this context, research on genomics and proteomics can help speed up the drug development process, taking a foothold in every stage of the drug discovery process and in clinical practice, ranging from drug target identification and validation, biomarker discovery and pharmacokinetics/pharmacodynamics analysis to toxicological studies. Among these disciplines, it becomes increasingly apparent that the proteomics will have a major role in creating a predictive, preventative, and personalized approach to medicine. Proteomics-based approaches have dominated the field, but still have faced many challenges due to technological limitations and biological complexity that were not expected before; more precisely, the detection limit of low-abundance proteins in plasma or sera and the presence of vast numbers of post-translational modified isoforms [1].

Diseased-cell secreted proteins/peptides offer several leads in biomarker development. Blood is a rich and universal source of biomarkers because of its proximity to all cells in the body. However, important physiological and practical aspects need consideration before serum peptidomics is effectively applied in a clinical, and later bedside, setting.

The need to identify disease biomarkers is critical to ensure fast diagnosis and timely treatment. Surface enhanced laser desorption/ionization time-of-fight mass spectrometry (SELDI-TOF-MS) is a widely used technology platform for diagnostic biomarker discovery. This short review provides an overview of how it functions and also describes its advantages and drawbacks.

This review summarises the screening methods from hepatic ultrasonography to serological biomarkers for early detection of liver cancer and focuses on evaluation of biomarkers ability. The development of novel biomarkers according to the 5-phase program defined by the Early Detection Research Network (EDRN) is also outlined in this review.

A monoclonal antibody, McAb9E (IgG3), was generated against a metastatic HCC cell line, MHCC-1. The antigen was characterized as human Caveolin-1 (Cav-1, 21kDa), with pI of 5.65. The Cav-1 antigen was found significantly over expressed in metastatic HCC cell lines as well as in tumor specimens. The Cav-1 specific McAb may be a useful molecular agent for metastatic HCC.

Proteasome subunit alpha type 7(PSMA7) is an α-type subunit of the 20S proteasome core complex and participates in degrading proteins through ubiquitin-proteasome pathway (UPP) which plays an important role in the regulation of cell proliferation or cell cycle control, transcriptional regulation, immune and stress response, cell differentiation, and apoptosis. Previous studies have demonstrated that PSMA7 can be a target interacting with some important proteins involved in transcription factor regulation, cell cycle transition, viral replication and even tumor initiation and progression, suggesting that PSMA7 could be a potential target for the development of clinical diagnosis and new therapeutic drugs. Here, we review the recent studies on PSMA7 involved in many different cellular processes, ranging from the cell cycle process to antigen processing and tumorigenesis.

Human chitinases (EC.3.2.1.14) are classified into family 18 of glycosyl hydrolase (GH18) superfamily based on their amino acid sequence similarities. Active chitinase hydrolyzes chitin, a β-1,4-linked N-acetyl-D-glucosamine oligosaccharide. Chitin is a major structural component of the insect exoskeletons and fungal cell walls, but is not found in vertebrates. In human, eight GH18 chitinases have been identified including active chitotriosidase and acidic mammalian chitinase. Most of the human chitinases lack chitinolytic activity due to mutation of an essential glutamic acid residue at the catalytic domain, and they are termed chitolectin. This review highlights some characteristics of human chitinases, compares structural differences among some human GH18 members, and discusses their cellular regulation and function. Finally, we summarize current views on the role of human chitinases in a variety of human diseases.

Aberrant glycosylation is frequently found in cancer, and efforts for biomarker discovery include the preparation of aberrant glycoproteins as promising analytes. Several lectins that bind to aberrant glycans and can be thus used to capture and enrich aberrant glycoproteins in the frontal stage during biomarker discovery are to be introduced.

Heat shock proteins (HSPs) consist of a large group of proteins with negligible expressions under physiological conditions. Their expressions are highly induced under stress conditions and they are ubiquitously expressed in various tissues and organs. HSPs possess chaperone functions, thus facilitating the correct folding of proteins or peptides. In hepatocellular carcinoma (HCC), high expressions of HSPs are demonstrated in liver cancer tissues and are correlated clinically with the severity of tumors and poor outcomes of HCC patients. This property enables them to be used as diagnostic markers for the onset of HCC. Since their expressions are highly expressed in liver cancer conditions, inhibitors or antisense oligonucleotides of HSPs are postulated to serve as potential therapeutics in treating this liver malignancy. In this review, we will first introduce the HSP family and discuss the major signaling pathways involved for the activities of HSPs. In addition, the clinical applications of HSPs in liver cancer in the aspects of diagnosis and therapy will be summarized and discussed.

Age- and stress-induced modulations in chaperone systems result in “chaperono-deficiency” or “chaperonopulence”. Development of modulators, of chaperone function has therefore, become an emerging field in drug development and discovery. This mini-review summarizes (i) the events leading to identification of an Hsp70 family stress chaperone, mortalin, (ii) experimental evidence to its role in old age diseases and cancer, and (iii) proposes it as a chaperonotherapeutic agent. As post-translational modifications and expression changes in mortalin are being explored as a biomarker for cancer, cardiovascular diseases and neurodegeneration, we discuss here how the current tools used in studying mortalin (e.g. antibodies, peptides, ribozymes, antisense and siRNA, recombinant proteins and small molecules etc.) could be creatively applied in a clinical setting to manage stress and to treat various chaperone-based maladies or “chaperonopathies”.

Hepatocellular carcinoma (HCC) is a malignant tumor unresponsive to most current therapies. Small peptides, either synthetic or derived from natural proteins, are found promising in treating HCC. Herein, different types of small peptides and their associated mechanistic actions against tumors are discussed, postulating their use as alternative treatments for HCC.

Bacterial endotoxin [e.g. lipopolysaccharide (LPS)] can trigger systemic hyper-inflammatory that subsequently leads to multiple organ failure and lethality (gram-negative sepsis). This paper describes the development of endotoxinneutralizing peptides that potentially treat sepsis. These peptides have been derived from bactericidal/permeabilityincreasing protein (BPIP), anti-microbial peptides, and leukocyte CD18 antigen and some of these peptides have been tested in clinical studies.

Five novel metalloproteinase protein inhibitors (MPIs) with molecular mass between 5.6 and 8.9 kDa and acid/neutral pI were detected in lupin seeds and exhibited strong inhibitory activities against thermolysin and/or gelatinase B. These novel peptides constitute not only the first MPIs described in plants but also the first plant peptides with inhibitory activity against a matrixin.

Prediction of protein secondary structure is somewhat reminiscent of the efforts by many previous investigators but yet still worthy of revisiting it owing to its importance in protein science. Several studies indicate that the knowledge of protein structural classes can provide useful information towards the determination of protein secondary structure. Particularly, the performance of prediction algorithms developed recently have been improved rapidly by incorporating homologous multiple sequences alignment information. Unfortunately, this kind of information is not available for a significant amount of proteins. In view of this, it is necessary to develop the method based on the query protein sequence alone, the so-called single-sequence method. Here, we propose a novel single-sequence approach which is featured by that various kinds of contextual information are taken into account, and that a maximum entropy model classifier is used as the prediction engine. As a demonstration, cross-validation tests have been performed by the new method on datasets containing proteins from different structural classes, and the results thus obtained are quite promising, indicating that the new method may become an useful tool in protein science or at least play a complementary role to the existing protein secondary structure prediction methods.

A set of 70 peptides with affinity for the class I MHC HLA-A*0201 molecule was subjected to quantitative analyses of structure-affinity relationship based on the SCORE function with good results (r2=0.6982, q2=0.6188, RMS=0.280). Then the ‘leave-one-out’ cross-validation (LOO-CV) and an outer test set including 18 outer samples were used to validate the QSAR model, and the results show that the QSAR model has good predictability for outside samples. Statistical analysis showed that the hydrophobic and hydrogen bond interaction played a significant role in peptide-MHC molecule binding. The study also provided useful information for structure modification of CTL epitope, and laid theoretical base for molecular design of therapeutic vaccine.