Editorial [Hot Topic: Protein Peptide Informatics and Drug Designing (Guest Editor: Rajani R. Joshi)]

Protein and Peptide Informatics offers enormous applications in deciphering of the molecular basis of diseases and in the discovery, design and delivery of biologically active and medicinally effective molecules. The past few decades have witnessed new horizons of research and a paradigm shift in drug designing strategies and technology development with promising achievements to leap ahead in the post-genomic era. This special issue of “Protein Peptide Letters” sketches a panorama of multi-dimensional research at the interface of Protein Peptide Informatics and Drug Designing with special focus on key approaches and innovative contributions emanated from Bioinformatics and Computational Biology.

Protein Kinases (PK) are drug-targets for treatment of several dreaded ailments including cancer and are of fundamental importance in modeling optimal drug activities because of their regulatory role in phosphorylation and ATP hydrolysis and hence in many signal transduction pathways in eukaryotes. Experimental studies of their catalytic reactions and inhibition have been integral parts of modern pharmaceutical research and development projects. The review paper by Ms. Anamika and Prof. N. Srinivasan adds a valuable contribution in this area. The bioinformatics and comparative analysis of PK families, their catalytic sequences and structural domains in two strains of Plasmodium presented here elucidate the molecular pathways and growth kinetics of this protozoan parasite which causes Malaria.

Statistical datamining of catalytic domain sequences of Protein Kinases carried out in my computational lab (c.f. paper by R. R. Joshi and Chaithanya M.) reveals some interesting facets of ‘selective conservation’ and flexibility of structural genomics of this special family of drug-targets.

In the past two decades, trend-setting initiatives have been put forth to understand the biological and pathogenic properties of the human T-cell stimulating viruses and suppressors and T-cell and B-cell epitopes of microorganisms and other antigenic carriers of diseases. Advancement of informatics of Immunogenetics and cellular and molecular Immuno-interactions has boosted emerging applications in anti-viral drug engineering and vaccine discovery. Recent developments focus upon peptide-drug design and computer aided vaccine synthesis. Six papers in this special issue deal with multidimensional research and development applications in this key area.

Ms A. D. Ozarkar and Profs. D Prakash, D. N. Deobagkar and D. D. Deobagkar have analyzed the structure of the Duffy binding like (DBLα) domain in Plasmodium falciparum Malaria Vaccine candidate var gene. Their predictions of likely T- and B- cell epitopes in this domain provide interesting implications and applications. A. D. Ghate, B. U. Bhagwat, S. B. Bhosle, S. M. Gadepalli and U. D. Kulkarni-Kale report development of a database and inference tools archiving molecular interactions of protein antigen-antibody. They have also shown good applications of this knowledgebase, named AgAbDb, in modifying the parameters for etimation of B-cell epitopes.

Thorough exploration of experiment data and knowledgebase requires mathematically or statistically sound algorithms. My paper on sequential eptiope prediction presents a new, computationally feasible and reliable algorithm of this sort with promising applications in vaccine development by peptide synthesis. The probabilistic model developed for this purpose also computes the binding correspondence between the sequences of predicted epitopes and complementarity determining regions (CDRs) of antibodies and thus provides a possible mode of interpreting the genomics of specificity and affinity of antigen - antibody interactions.

Experimental investigations of S.S. Dewasthaly, G.S. Bhonde, V.S. Raman, S. M. Biswas, V.M. Ayachit, and Dr. M.M. Gore identify T-cell stimulating and MAb binding peptide epitopes from envelope glycoprotein (Egp) and NS-1 and Mem proteins of Japanese Encephalitis Virus in mice. Derived from these results the authors report Chimeric T helper- B cell peptides for effective vaccination..........