Computational and Structural Biotechnology Journal 13 (2015) 204–211 Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/csbj Mini review Advances in the development of SUMO specific protease (SENP) inhibitors Ashutosh Kumar 1, Kam Y.J. Zhang ⁎ Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan article info abstract Article history: Sumoylation is a reversible post-translational modification that involves the covalent attachment of small Received 1 February 2015 ubiquitin-like modifier (SUMO) proteins to their substrate proteins. Prior to their conjugation, SUMO proteins Received in revised form 6 March 2015 need to be proteolytically processed from its precursor form to mature or active form. SUMO specific proteases Accepted 16 March 2015 (SENPs) are cysteine proteases that cleave the pro or inactive form of SUMO at C-terminus using its hydrolase Available online 24 March 2015 activity to expose two glycine residues. SENPs also catalyze the de-conjugation of SUMO proteins using their Keywords: isopeptidase activity, which is crucial for recycling of SUMO from substrate proteins. SENPs are important for Sumoylation maintaining the balance between sumoylated and unsumoylated proteins required for normal cellular physiolo- SUMO gy. Several studies reported the overexpression of SENPs in disease conditions and highlighted their role in the SENP development of various diseases, especially cancer. In this review, we will address the current biological under- Prostate cancer standing of various SENP isoforms and their role in the pathogenesis of different cancers and other diseases. We Virtual screening will then discuss the advances in the development of protein-based, peptidyl and small molecule inhibitors of various SENP isoforms. Finally, we will summarize successful examples of computational screening that allowed the identification of SENP inhibitors with therapeutic potential. © 2015 Kumar and Zhang. Published by Elsevier B.V. on behalf of the Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Contents 1. SUMOandsumoylation......................................................... 204 2. SENPandSENPisoforms........................................................ 205 3. RoleofSENPsinthedevelopmentofvariousdiseases........................................... 206 4. IdentificationofSENPinhibitors..................................................... 207 5. Computational approaches in the identificationofSENPinhibitors...................................... 208 6. Concludingremarks........................................................... 210 Acknowledgments.............................................................. 210 References................................................................. 210 1. SUMO and sumoylation packing and dynamics, genome integrity, nuclear transport, signal trans- duction and cell proliferation [1–5]. In sumoylation SUMO proteins are Sumoylation is a reversible process that involves the post- covalently attached to the ε-amino group of lysine residues in specific translational modification of target proteins with an approximately target proteins via an enzymatic cascade that requires a sequential action 10 kDa small ubiquitin-like modifier (SUMO) protein. Sumoylation is of an activating enzyme E1, a conjugating enzyme E2 and a ligase E3 an important mechanism regulating the activities of various proteins in- [1–5] (Fig. 1A). The first step in the sumoylation pathway involves the volved in cellular processes like DNA replication and repair, chromosome conjugation of a SUMO protein to SUMO activating enzyme 1 (SUMO E1) that starts with the binding of ATP. The SUMO E1 subsequently catalyzes the adenylation of SUMO C-terminus at the expense of ATP to ⁎ Corresponding author. Tel.: +81 45 503 9560; fax: +81 45 503 9559. E-mail address: [email protected] (K.Y.J. Zhang). form SUMO-AMP intermediate. Following the formation of SUMO-AMP 1 Tel.: +81 45 503 9560; fax: +81 45 503 9559. intermediate, the catalytic residue Cys173 on SUMO E1 and SUMO- http://dx.doi.org/10.1016/j.csbj.2015.03.001 2001-0370/© 2015 Kumar and Zhang. Published by Elsevier B.V. on behalf of the Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). A. Kumar, K.Y.J. Zhang / Computational and Structural Biotechnology Journal 13 (2015) 204–211 205 Fig. 1. Sumoylation and desumoylation pathway. (A) In sumoylation, SUMO protein is covalently attached to lysine residues in target proteins via a sequential action of an activating enzyme E1, a conjugating enzyme E2, and a ligase E3. (B) SENPs possess endopeptidase activity to carry out proteolytic processing at the precursor SUMO C-terminus (SUMO-2 C-terminus is shown here) to expose two glycine residues. SENPs also possess isopeptidase activity to release conjugated SUMO from substrate proteins. AMP intermediate came close as the result of a large conformational 2. SENP and SENP isoforms change in SUMO E1 [6] which is followed by the transfer of SUMO to the catalytic residue Cys173 on SUMO E1 by the formation of a thioester Mammalian cells express four SUMO isoforms: SUMO-1, SUMO-2, bond between SUMO C-terminus and Cys173 [6–8]. The next step SUMO-3 and SUMO-4. The mammalian SUMO-2 and SUMO-3 are involves the subsequent transfer of SUMO protein from SUMO E1 to much more similar to each other than to SUMO-1. SUMO-4 on the SUMO E2 (also known as Ubc9); again with the formation of a thioester other hand is highly homologous with SUMO-2 and SUMO-3, but its ex- linkage between the C-terminal glycine in SUMO protein and the pression is limited only to a few tissues and organs, mainly the kidney, catalytic Cys93 in SUMO E2. Ubc9 is the only known SUMO E2 enzyme, lymph and spleen [15,16]. SUMO proteins are expressed as precursors and its deletion abolishes SUMO conjugation [9–11]. In the last step, and need to be proteolytically processed from its pro or inactive form Ubc9 catalyzes the covalent attachment of the SUMO protein to the to mature form [4,17–21]. Sentrin/SUMO-specific proteases (SENPs) ε-amino group in a specific lysine residue of substrate proteins. SUMO cleave inactive or pro form of SUMO at the C-terminus via its hydrolase E3 ligase increases the efficiency of this step by associating with both activity to expose two glycine residues and thereby generating active or the substrate protein and Ubc9 [12–14]. mature SUMO (Fig. 1B) [4,17–21].InadditiontoC-terminalproteolytic 206 A. Kumar, K.Y.J. Zhang / Computational and Structural Biotechnology Journal 13 (2015) 204–211 processing, SENPs also possess isopeptidase activity that is essential for the functional activity [26]. SUMO proteins enter the catalytic site via the recycling of SUMO proteins [4,17–21]. These enzymes specifically a narrow tunnel lined by Trp residues, which are essential for the accu- cleave the isopeptide bond between the C-terminal glycine of SUMO rate positioning of Gly–Gly motif and sessile bond. It has been revealed and the substrate protein lysine thereby releasing the SUMO protein that the sessile bond is oriented in a cis-configuration that creates a kink from its substrate (Fig. 1B). in SUMO precursor tails and isopeptide linkage of sumoylated substrate Six SENP isoforms (SENP1, SENP2, SENP3, SENP5, SENP6 and SENP7) proteins. These types of cis-peptide bonds are not stable and promote have been identified in mammals. These six SENPs can be divided into cleavage [25]. three sub-families based on their sequence homology, substrate speci- ficity and subcellular localization as shown in Table 1 [4,17–21]. 3. Role of SENPs in the development of various diseases SENP1 and SENP2 constitute the first family and have broad specificity for SUMO-1/2/3. SENP3 and SENP5 form the second family, while the SENP enzymes play a critical role in maintaining normal cellular third family has SENP6 and SENP7 as its members. Apart from SENP1 physiology by preserving the balance between sumoylated and and SENP2, all other SENP isoforms prefer SUMO-2/3 over SUMO-1 for unsumoylated proteins. Knockout studies in mice have shown that the deconjugation. The posttranslational modification of substrate proteins absence of SENP1 or SENP2 is embryonically lethal [31,32]. However by SUMO-4 has not been observed due to SENP's inability to proteolyt- in diseased states, this balance between SUMO modified and non- ically process SUMO-4 precursor in vivo [16,22]. The maturation of pre- modified proteins is disrupted due to the altered expression of SENPs. cursor SUMO-4 seems to be inhibited by the presence of Pro90 residue Several studies implicated the role of various SENP isoforms in the de- in place of Gln in SUMO-1–3. Pro90 causes conformational constraint velopment of various diseases, including prostate cancer [31,33–35], and makes the peptide bond to be cleaved inaccessible to the narrow thyroid cancer [36], colon cancer [37], pancreatic cancer [38], athero- active site of SENP [22,23]. A P50Q single amino acid mutation made sclerosis [39] and heart diseases [40]. Especially, numerous studies indi- the precursor SUMO-4 amenable to SENP2 processing while another ad- cated the role of SENPs in prostate cancer development. Androgen ditional mutation G63D made it a highly efficient SENP2 substrate