Original article Analysis of physico-chemical properties of substrates of ABC and MFS multidrug transporters of pathogenic Candida albicans Nidhi Puri a,1 , Om Prakash b,1 , Raman Manoharlal a , Monika Sharma a , Indira Ghosh b , Rajendra Prasad a, * a Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India b School of InformationTechnology, Jawaharlal Nehru University, New Delhi-110067, India article info Article history: Received 11 February 2010 Received in revised form 20 July 2010 Accepted 27 July 2010 Available online 10 August 2010 Keywords: Candida albicans ABC transporter Descriptors Substrate MFS transporter abstract In this study, we have explored the structure activity relationships of substrates of two major, promis- cuous, multidrug transporters of an opportunistic human pathogen Candida albicans namely, CaCdr1p and CaMdr1p. To differentiate between substrates and non-substrates, the susceptibilities of the Saccharomyces cerevisiae strains over-expressing CaCdr1p or CaMdr1p were determined for 67 struc- turally diverse xenobiotics. A comparison of physico-chemical indices of these tested compounds enabled identification of molecular descriptors such as, degree of hydrophobicity (MLogP), geometrical descriptor (DISPv), molecular edge descriptor (MDEC.12 and MDEC.13) and 3D-Morse descriptors, that allowed their segregation into substrates and non-substrates for both the transporter proteins. Taken together, present study provides first evidence of chemical basis of substrate specificities of two clinically relevant multidrug transporters of an opportunistic human pathogen C. albicans. Ó 2010 Elsevier Masson SAS. All rights reserved. 1. Introduction Current evidences suggest that pathogenic Candida albicans acquires azole resistance by employing multiple mechanisms and these include (a) failure of drug accumulation mediated by extru- sion pump proteins such as CaCdr1p and CaCdr2p belonging to ATP Binding Cassette (ABC), and CaMdr1p belonging to Major Facilitator Family (MFS) super families; (b) alterations in the azole target protein Erg11p; as well as (c) up regulation of the ERG11 gene [1e6]. ABC family proteins are primary active transporters, pumping their substrates including small molecules and macromolecules, up a concentration gradient powered by ATP hydrolysis while the MFS transporters are secondary carriers capable of transporting small solutes in response to chemi-osmotic ion gradients [7]. A typical ABC protein such as CaCdr1p in C. albicans comprises of four core domains; two transmembrane domains (TMDs) that form the permeation pathway for translocation of a substrate and two nucleotide binding domains (NBDs) that hydrolyze ATP to power this process. Each TMD is comprised of six transmembrane segments (TMS) which are envisaged to confer substrate specificity [8e10]. The nature of substrates varies enormously, as it includes structurally unrelated compounds such as azoles, lipids and steroids [11]. The proton-antiporter CaMdr1p belonging to MFS family which has been identified and characterized in C. albicans also transports various substrates of diverse structures. Interest- ingly, both CaCdr1p and CaMdr1p are functionally similar (extrude drugs) but differ mechanistically in terms of their mode of energy coupling to drug transport [12]. Both these export proteins also differ in their lipid specificities. For example, while CaCdr1p prefers to be localized in detergent resistant micro domains (rafts) of plasma membrane, no such preference is shown by CaMdr1p [13]. CaCdr1p and CaMdr1p also differ in their ability to translocate membrane phospholipids between the two lipid mono layers wherein only the former elicits floppase activity [11,14]. Notwith- standing the differences in energy coupling and lipid preferences elicited by CaCdr1p and CaMdr1p, they both show promiscuity towards substrates they export. Therefore, considerable attention is being devoted towards assessment of the structural and functional features in these proteins which could explain their diverse substrate specificity spectrum. Understanding SAR between these proteins and host of xenobiotics they export is expected to help in designing improved strategies to develop modulators/inhibitors of these clinically relevant pump proteins. Abbreviations: ABC, ATP-binding cassette; MFS, Major Facilitator Super family; TMD, transmembrane domains; NBD, nucleotide binding domains; RF, Random Forest; OOB, Out of Bag; MDE, Molecular distance edge; SAR, Structure activity relationship; CV, cross-validated. * Corresponding author. Tel.: þ91 11 2670 4509; fax: þ91 11 2674 1081. E-mail address: rp47jnu@gmail.com (R. Prasad). 1 Both the authors have contributed equally to this study. Contents lists available at ScienceDirect European Journal of Medicinal Chemistry journal homepage: http://www.elsevier.com/locate/ejmech 0223-5234/$ e see front matter Ó 2010 Elsevier Masson SAS. All rights reserved. doi:10.1016/j.ejmech.2010.07.050 European Journal of Medicinal Chemistry 45 (2010) 4813e4826