Comparative genomics allowed the identification of drug targets against human fungal pathogens

Abadio et al. BMC Genomics 2011, 12:75 http://www.biomedcentral.com/1471-2164/12/75 RESEARCH ARTICLE Open Access Comparative genomics allowed the identification of drug targets against human fungal pathogens Ana Karina R Abadio1,3, Erika S Kioshima1, Marcus M Teixeira1, Natalia F Martins2, Bernard Maigret3, Maria Sueli S Felipe1* Abstract Background: The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed people. These patients present severe clinical forms of the infections, which are commonly fatal, and they are more susceptible to opportunistic fungal infections than non-immunocompromised people. IFIs have historically been associated with high morbidity and mortality, partly because of the limitations of available antifungal therapies, including side effects, toxicities, drug interactions and antifungal resistance. Thus, the search for alternative therapies and/or the development of more specific drugs is a challenge that needs to be met. Genomics has created new ways of examining genes, which open new strategies for drug development and control of human diseases. Results: In silico analyses and manual mining selected initially 57 potential drug targets, based on 55 genes experimentally confirmed as essential for Candida albicans or Aspergillus fumigatus and other 2 genes (kre2 and erg6) relevant for fungal survival within the host. Orthologs for those 57 potential targets were also identified in eight human fungal pathogens (C. albicans, A. fumigatus, Blastomyces dermatitidis, Paracoccidioides brasiliensis, Paracoccidioides lutzii, Coccidioides immitis, Cryptococcus neoformans and Histoplasma capsulatum). Of those, 10 genes were present in all pathogenic fungi analyzed and absent in the human genome. We focused on four candidates: trr1 that encodes for thioredoxin reductase, rim8 that encodes for a protein involved in the proteolytic activation of a transcriptional factor in response to alkaline pH, kre2 that encodes for a-1,2-mannosyltransferase and erg6 that encodes for Δ(24)-sterol C-methyltransferase. Conclusions: Our data show that the comparative genomics analysis of eight fungal pathogens enabled the identification of four new potential drug targets. The preferred profile for fungal targets includes proteins conserved among fungi, but absent in the human genome. These characteristics potentially minimize toxic side effects exerted by pharmacological inhibition of the cellular targets. From this first step of post-genomic analysis, we obtained information relevant to future new drug development. Background 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 * Correspondence: 1 Department of Cellular Biology, University of Brasília, Brasília, Brazil Full list of author information is available at the end of the article by opportunistic fungi than non-immunocompromised people [3]. 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 [4]. 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 © 2011 Abadio et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abadio et al. BMC Genomics 2011, 12:75 http://www.biomedcentral.com/1471-2164/12/75 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 [5]. 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 P450 enzymes [6]. 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 [7]. 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 [11]. 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 genomewide 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 [12]. 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 Inst (...truncated)