The frequency and diversity of invasive fungal infections have changed over the last 25 years. The emergence of less common, but medically important, fungi has increased, especially in the large populations of immunocompromised patients and of those hospitalized with serious underlying diseases [1, 2]. These patients develop more severe clinical forms of mycoses, which are commonly fatal, and they are more susceptible to infections by opportunistic fungi than non-immunocompromised people . The antifungal agents currently available for the treatment of systemic mycoses include four groups of drugs: polyenes (amphotericin B), azoles (fluconazole, itraconazole, ketoconazole, posaconazole and voriconazole), echinocandins (caspofungin, anidulafungin, and micafungin) and flucytosines . Conventional amphotericin B, despite being a broad-spectrum fungicidal agent with little intrinsic or acquired resistance, is limited by its serious toxicities and lack of an oral formulation for systemic therapy. In recent years, three lipid formulations of amphotericin B (amphotericin B lipid complex, amphotericin B cholesteryl sulfate and liposomal amphotericin B) have been developed and approved by the Food and Drug Administration (FDA). Although less nephrotoxic than deoxycholate amphotericin B, lipid amphotericin B nephrotoxicity still limits treatment compared to the newer triazoles and echinocandins . The triazoles are the most widely used antifungal agents and have activity against many fungal pathogens, with less serious nephrotoxic effects observed than with amphotericin B. However, the azoles antifungals have many drug-drug interactions with multiple drug classes owing to their interference with hepatic cytochrome P-450 enzymes . Another problem with azoles therapy is the acquired resistance of many pathogens to these drugs, which is the most common cause of refractory infection. Thus, the search for alternative therapies and/or the development of more specific drugs is a challenge. Recently, efforts have been devoted to the chemistry side of discovering new antifungal agents, including the development of third-generation azoles or a new therapeutic class of antifungal drugs, such as echinocandins . Additionally, nanotechnology approaches have improved the development of innovative products that reduce side effects by lowering dose administration of already available drugs, such as amphotericin B nanoencapsulated [8–10]. Many advances have been made in antifungal drug development in the past decade. However, the search for more specific drugs, in an effort to overcome the global problem of resistance to antifungal agents and minimize the serious side effects, is increasingly relevant and necessary.
Currently, drug research and development are expensive and time consuming. An estimated 14 years and an average of $1.8 billion is the investment required to develop a new drug that will reach the market . Selecting new molecular targets by comparative genomics, homology modeling and virtual screening of compounds is promising in the process of new drug discovery. In fact, technological advances over the past two decades have led to the accumulation of genome-wide sequence data for many different fungal species. As the number of sequenced genomes rapidly increases, searching and comparing sequence features within and between species has become a part of most biological inquires . Currently, 183 fungi genomes have been sequenced, either completely or are in the process of sequencing, and 40 human pathogenic fungi genomes have been sequenced. (Data collected on 09/07/2010 in the following databases: Fungal Genomes, TIGR, Sanger, Broad Institute and NCBI). Seven of the human pathogens are of great importance in systemic mycosis: Candida albicans, Aspergillus fumigatus, Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, Paracoccidioides brasiliensis and Histoplasma capsulatum, which are strong candidates for post-genomic studies.
Comparative genomics strategy is a useful tool in identifying potential new drug targets, such as putative essential genes and/or those affecting the cell viability that are conserved in pathogenic organisms [13–16]. By this methodology, ten genes conserved in three bacteria species (Staphylococcus aureus, Mycobacterium tuberculosis and Escherichia coli 0157: H7) were selected as candidates for an antibacterial drug . Since the publication of the nematode Brugia malayi complete genome, Kumar and colleagues  conducted a comparison analysis between the genomes of B. malayi and Caenorhabditis elegans and were able to identify 7,435 orthologs genes, from which 589 were identified as essential, as well as absent in the human genome, resulting in a list of candidate target genes for new drug development. Recently, Caffrey and colleagues  identified new drug targets in the metazoan pathogen Schistosoma mansoni, the causative agent of Schistosomiasis. The authors identified 35 orthologs essential genes and potential drug targets against this human pathogen.
Here we identified potential drug targets applied to human fungal pathogens using comparative genomics strategy. Ten genes were present in all pathogenic fungi analyzed and absent in the human genome. Among them, four genes (trr1, rim8, kre2 and erg6) were selected for future research and new drug development. Two of those genes codify for proteins (TRR1 and KRE2) that showed significant identity when compared to templates already deposited in the databank PDB (Protein Database Bank), which were used to perform homology modeling of both enzymes. These results will be used to virtually screen combinatorial libraries, offering new perspectives on technological development and innovation of antifungal agents against human pathogens.