Novel Compounds Identified by Structure-Based Prion Disease Drug Discovery Using <i>In Silico</i> Screening Delay the Progression of an Illness

Abstract

The accumulation of abnormal prion protein (PrPSc) produced by the structure conversion of PrP (PrPC) in the brain induces prion disease. Although the conversion process of the protein is still not fully elucidated, the intramolecular chemical bridging in the most fragile pocket of PrP, known as the “Hot Spot”, can stabilize the structure of PrPC and inhibit the conversion process. Using our original structure-based drug discovery algorithm, we identified the low molecular weight compounds that can bind to the hot spot. Several candidates were identified as anti-prion drugs with strong binding to recombinant PrP in vitro that significantly reduced the levels of PrPSc. These compounds were able to decrease the number of aggresomes in persistently prion-infected cells. Remarkably, treatment with the predominant candidate compounds significantly prolonged the survival period of prion-infected mice and dominantly suppressed disease-specific pathological damage, such as vacuole degeneration, PrPSc accumulation, microgliosis and astrogliosis in the brain, suggesting their possible clinical use. Fragment molecular orbital (FMO) analysis indicated that the high affinity of the candidates to the protein is largely dependent on non-polar interactions, such as van der Waals interactions. Our results suggest that in silico drug discovery using NUDE/DEGIMA may be useful to identify candidate compounds that effectively stabilize the protein. Funding Statement: This work was supported in part by the a grant from a Grant-in-Aid of the Research Committee of Prion Disease and Slow Virus Infection from the Ministry of Health, Labour and Welfare of Japan (N.N.); a Grant-in-Aid of the Research Committee of Molecular Pathogenesis and Therapies for Prion Disease and Slow Virus Infection, the Practical Research Project for Rare and Intractable Disease from the Japan Agency for Medical Research and Development, AMED (D.I.); a grant from the Takeda Science Foundation (N.N. and D.I.); a grant from the Japan Intractable Disease Research Foundation (D.I.); a Grant-in-Aid from the Tokyo Biochemical Research Foundation (D.I.); a grant provided by the YOKOYAMA Foundation for Clinical Pharmacology (Grant No. YRY1502) (D.I.); the grant provided by the Ichiro Kanehara Foundation (D.I.); a grant provided by the Mochida Memorial Foundation for Medical and Pharmaceutical Research (D.I.); a grant provided by the Waksman Foundation of Japan Inc. (D.I.); and a grant provided by the Center for Clinical and Translational Research of Kyushu University Hospital (D.I.). Declaration of Interests: The authors state that they have no conflicts of interest. Ethics Approval Statement: Animal experiments were approved by the Animal Care and Use Committee of the Nagasaki University. All animals were treated and cared for in accordance with the Guidelines for Animal Experimentation of Nagasaki University.