title: Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease.
abstract: Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.|Biophysics Graduate Group, University of California, San Francisco, CA, 94158-2280, USA.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Gable
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
authors.forename: Gregory M
authors.identifier: http://orcid.org/0000-0002-2398-6648
authors.initials: GM
authors.lastname: Lee
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Acker
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.|Chemistry and Chemical Biology Graduate Group, University of California, San Francisco, CA, 94158-2280, USA.
authors.forename: Kaitlin R
authors.initials: KR
authors.lastname: Hulce
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Gonzalez
authors.affiliation: Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schweigler
authors.affiliation: Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland.
authors.forename: Samu
authors.initials: S
authors.lastname: Melkko
authors.affiliation: Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Farady
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA. Charles.Craik@ucsf.edu.
authors.forename: Charles S
authors.initials: CS
authors.lastname: Craik
mesh_terms: D004305:Dose-Response Relationship, Drug; D019288:Herpesvirus 8, Human / Q000201:enzymology*; D057166:High-Throughput Screening Assays; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D010447:Peptide Hydrolases / Q000378:metabolism*; D011480:Protease Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D011485:Protein Binding / Q000187:drug effects; D012697:Serine Endopeptidases / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D011480:Protease Inhibitors; D010447:Peptide Hydrolases; D012697:Serine Endopeptidases; C071910:assemblin
keywords: NMR spectroscopy; dimer disruption; fragment-based screening; human herpesviruses; proteases
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