Protease substrates to protease inhibitors

Protease substrates to protease inhibitors

HIV-1 protease inhibitors

Aim

To design and synthesize inhibitors to the aspartyl HIV-1 protease. To generate leads with high potency, selectivity and fair bioavailability for further development. To develop a strategy that allows production at a low cost.

 

Method

Structure-based design. The compounds synthesized are cocrystalized with the protease and the structural information guides us in further design in an iterative fashion. A large number of very potent transition-state analogues that have been extensively studied in vitro and in vivo have been developed. The relation between the chemical structures of these and the oral bioavailability is studied within the group at BMC. Inexpensive carbohydrates are used as chiral pools. We use stereoselective methods for creation of libraries of masked tert-OH based inhibitors. Development of new microwave-enhanced high-speed synthesis methods are in progress.

Plasmepsin inhibitors

Status

Established Project

 

Indication

Malaria

 

Background

Four different species cause malaria in man. Malaria is a disease of world-wide impact, afflicting several hundred million and killing nearly two million people each year. Resistance to current drugs such as chloroquine and mefloquine is spreading rapidly and our anti-malarial armamentarium is almost depleted. Ten aspartic proteases are encoded in the most lethal malaria species, Plasmodium falciparum. Three of these, plasmepsin I, II and IV, are known to be involved in the hemoglobin degradation in the parasite food vacuole and are novel targets for anti-malarial drug discovery. In the other three human malaria parasites, only the orthologue to plasmepsin IV in P. falciparum (PfPM4) has been identified. Thus, it is likely that an inhibitor of PfPM4 would reduce parasitic growth, regardless of the infecting species.

 

Aim

To design and prepare transition-state based inhibitors to the aspartic proteases plasmepsin I, II, IV and the corresponding isoenzymes in P. vivax, P. malariae and P. ovale. Generation of leads structures with high potency, bioavailability and adequate selectivity for further development.

 

Method

Bioavailability issues and selectivity versus mammalian cathepsin D will be taken into account at an early stage of the discovery process. Plasmepsin II and IV are our main targets. Crystal structures of PfPM2, PfPM4, PmPM4 and PvPM4 complexed with various inhibitors are available. Computational modeling combined with information on the substrate structures has enabled us to design a series of low molecular weight peptidomimetic inhibitors. Biased libraries of sterically masked mono-hydroxy transition-state analogues will be synthesized. Microwave chemistry will be used both for production of starting material and for lead optimization.

Hepatitis C virus protease inhibitors

Status

Established Project

 

Indication

Hepatitis C

 

Background

Hepatitis C virus (HCV) is the major etiological agents of post transfusion and sporadic community-acquired non-A, non-B hepatitis. In the majority of cases, HCV causes a persistent liver infection that eventually develops into cirrhosis or hepatocellular carcinoma. As a consequence, HCV is the major indication for liver transplantation in the western countries. Chronic HCV infection is a global disease, and the number of carriers is estimated to be about 170 million. In Europe and Japan, the disease is more prevalent than either hepatitis B or HIV infections. We address the hepatitis C virus NS3 serine protease. This protease is essential for the production of infectious virus and hence represents a target for the development of inhibitors. Proof-of-concept in early clinical trials of NS3 protease inhibitors has been achieved. At the same time indications of a rapid development of resistance have emerged, which stress the need for drugs with unique chemical structures and resistance profiles.

 

Aim

To design and synthesize protease inhibitors of the viral full-length NS3 protein (protease-helicase/NTPase). Generation of leads with high potency, selectivity, unique resistance profiles and fair bioavailability for further development.

 

Method

We elaborate on the N-terminal region of the substrate and employ combinatorial technologies for lead generation. Structural information is gathered from the available X-ray structure of the full-length NS3 protein (protease-helicase/NTPase). 3D-QSAR (COMFA) and computational modeling combined with systematic investigation and replacement of peptide fragments with peptidomimetic prosthetic units and different bioisosteres will be employed. A subgoal is to obtain new inhibitors that can be cocrystallized with the protease thereby enabling a more efficient structure-based drug design approach.

Inhibitors of β-secretase

Status

New Project

 

Indication

Alzheimer's disease

 

Background

Alzheimer's disease (AD) is a neurodegenerative disease of the brain that is characterized by the progressive formation of insoluble amyloid plaques and fibrillary tangels. Plaques are extracellular constructs consisting primarily of aggregated Aβ42, a peptide fragment formed by the sequential proteolytic processing of β-amyloid precursor protein (APP) by two enzymes, β- and γ-secretase. β-Secretase (β-site APP cleaving enzyme or BACE-1), a novel type I transmembrane aspartyl protease whose identity remained elusive until 1999, is believed to be the key enzyme that commits APP catabolism to the amyloidogenic pathway. The amyloid hypothesis for treatment of Alzheimer's disease holds that inhibition of BACE-1 should hinder deposition of long Aβ peptides and stop subsequent plaque formation in the brain. The majority of the BACE-1 inhibitors that have appeared in the literature are peptide-based analogues that replace the scissile amide bond with a noncleavable isostere mimicking the transition-state for the amide bond cleavage. Potent enzymatic inhibition has been achieved but the peptidic character of the inhibitors precludes their use as therapeutic agents. The principal challenge is the construction of drug-like molecules that exhibit both high bioavailability and ability to cross blood-brain barrier (BBB) but still retaining Ki values in the nanomolar range in enzyme assays.

 

Aim

To design and synthesize selective and bioavailable non-peptidic β-secretase inhibitors. To investigate different strategies for masking the transition-state mimicking isostere.

 

Method

Molecular modelling, enzyme-inhibitor docking and other computational methods, including molecular dynamic simulations, will guide the design process. Stereoselective synthetic strategies that allow for a systematic investigation and replacement of peptidomimetic prosthetic units carrying different bioisosteres will be employed. Side-chains will be optimized by high-speed chemistry techniques.