DOI: 10.1002/cmdc.201000133 Discovery of a Class of Diketopiperazines as Antiprion Compounds Maria Laura Bolognesi,* [a] Hoang Ngoc Ai Tran, [b] Matteo Staderini, [c] Alessandra Monaco, [c] Alberto López-CobeÇas, [c] Salvatore Bongarzone, [d, e] Xevi BiarnØs, [d, e] Pilar López-Alvarado, [c] Nieves Cabezas, [c] Maria Caramelli, [f] Paolo Carloni, [d, e, g] J. Carlos MenØndez, [c] and Giuseppe Legname [b, e] Introduction Prion diseases, also known as transmissible spongiform ence- phalopathies (TSEs), are neurodegenerative and infectious dis- orders that affect both humans and animals, and are not cura- ble with drugs. Although reliable proof-of-principle was dem- onstrated in a variety of experimental models, and several small molecules have been identified as active against TSE (for a review, see Reference [1]), the mode-of-action and targets for most of these molecules remain largely unexplored. As a result, drugs effective against this process are still years away from approval. [2] There are two main reasons why drug discov- ery for the treatment of prion diseases has not progressed as rapidly as in other pharmaceutical fields. First, human prion diseases are very rare. Each year, only approximately 300 people in the USA and approximately 100 people in the UK succumb to various forms of prion disease. [3] Nevertheless, these disorders have come to public and scientific attention due to the fact that they can be transmissible among humans and, under particular conditions, from animals to humans. The emergence of a Creutzfeld–Jakob disease (CJD) variant in the 1990s demonstrated the transmissibility of bovine spongiform encephalopathy to humans and set the scene for a hypotheti- cal epidemic scenario. [3] Second, TSE is a conformational dis- ease, [4] where the cellular form of the prion protein (PrP C ) is converted to a misfolded variant (PrP Sc ) through a nucleated polymerization process. [5] This pathological conformational transition of the prion protein (PrP) results in a decrease in part of the a-helical folding and a concomitant increase in the b-sheet content of PrP Sc . As seen in other amyloidoses, [6] the PrP Sc isoform displays a pronounced resistance to proteases and is prone to forming aggregates. All of these features lead to the main biological difference between the two prion pro- teins: PrP Sc is infectious, whereas PrP C is not. [7] From a medicinal chemistry perspective, all conformational diseases are ‘black boxes’ because the knowledge of the three- dimensional structure and mechanistic properties of the target, fundamental prerequisites in modern drug discovery, are [a] Prof. M. L. Bolognesi Department of Pharmaceutical Sciences, University of Bologna Via Belmeloro 6, 40126 Bologna (Italy) Fax: (+ 39) 051-209-9734 E-mail : marialaura.bolognesi@unibo.it [b] H. N. Ai Tran, + Prof. G. Legname Laboratory of Prion Biology, Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati–International School of Advanced Studies (SISSA-ISAS), Area Science Park, Basovizza, 34151 Trieste (Italy) [c] M. Staderini, + A. Monaco, A. López-CobeÇas, P. López-Alvarado, N. Cabezas, Prof. J. C. MenØndez Departamento de Química Orgµnica y FarmacØutica University of Madrid (Spain) [d] S. Bongarzone, Dr. X. BiarnØs, Prof. P. Carloni Statistical and Biological Physics Sector, Scuola Internazionale Superiore di Studi Avanzati–International School for Advanced Studies (SISSA-ISAS), 34151 Trieste (Italy) [e] S. Bongarzone, Dr. X. BiarnØs, Prof. P. Carloni, Prof. G. Legname SISSA unit, Italian Institute of Technology, 34151 Trieste (Italy) [f] Dr. M. Caramelli Istituto Zooprofilattico Sperimentale Torino, 10154 Torino (Italy) [g] Prof. P. Carloni German Research School for Simulation Sciences GmbH, Forschungzentrum Jülich GmbH–RWTH Aachen University, Aachen, (Germany) [ + ] These authors equally contributed to the experimental work. Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.201000133. Prion diseases are fatal neurodegenerative and infectious dis- orders for which effective pharmacological tools are not yet available. This unmet challenge and the recently proposed in- terplay between prion diseases and Alzheimer’s have led to a more urgent demand for new antiprion agents. Herein, we report the identification of a novel bifunctional diketopiper- azine (DKP) derivative 1d, which exhibits activity in the low mi- cromolar range against prion replication in ScGT1 cells, while showing low cytotoxicity. Supported by properly addressed molecular modeling studies, we hypothesized that a planar conformation is the major determinant for activity in this class of compounds. Moreover, studies aimed at assessing the mechanism-of-action at the molecular level showed that 1d might interact directly with recombinant prion protein (recPrP) to prevent its conversion to the pathogenic misfolded prion protein (PrP Sc )-like form. This investigation suggests that DKP based antiprion compounds can serve as a promising lead scaffold in developing new drugs to combat prion diseases. 1324  2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim ChemMedChem 2010, 5, 1324 – 1334 MED