Bach Group

The PPI targets we focus on are involved in redox signalling, oxidative stress, and inflammation - both inside and outside the central nervous system (CNS). Thereby, they play important roles in numerous and various diseases such as multiple sclerosis, stroke, acute lung inflammation, rheumatoid arthritis, and some cancers.

Our main targets are Keap1, which regulates Nrf2 and thereby the endogenous antioxidant response, and the superoxide-generating multi-subunit enzyme complex NADPH oxidase 2 (NOX2). Recently, we initiated work on the cytokine tumor necrosis factor (TNF) and new projects including novel cancer-related PPI targets.

We screen our libraries of fragments (small substructures of drug-like molecules) by biochemical and sensitive biophysical methods (FP, SPR, ligand-based NMR). Promising hits are optimized into lead compounds by medicinal chemistry, X-ray crystallography, and pharmacological assays.

1.  For Keap1, we analysed known inhibitors for their ability to cross the blood-brain barrier (Pallesen et al, 2018, J Med Chem). This was followed by a comparative assessment study, where the compounds from literature were tested in a range of assays to validate and compare their activity towards Keap1. Interestingly, about half of the reported Keap1 inhibitors were found to be false positives (Tran and Pallesen et al, 2019, J Med Chem and Derek Lowe’s blog).
   

   

2. We have addressed Keap1 by FBDD pursuing three strategies: First, we deconstructed the known compounds into a target-biased library of 77 fragments and tested them for Keap1 binding using four orthogonal biophysical assays. The binding modes of key fragment hits were determined by X-ray crystallography, which allowed us to merge two fragments into novel compounds with high affinities to Keap1 (Pallesen et al, 2021, J. Med. Chem; see also Practical Fragments blog). Secondly, we screened our commercial library of 2,500 fragments using four orthogonal methods. X-ray crystallography and medicinal chemistry resulted in a 1700-fold affinity-increase going from fragment to lead (Narayanan and Tran et al, 2022, J Med Chem; see also MAX IV’s news article). Thirdly, we screened the Diamond Light Source’s XChem library by X-ray crystallography and are currently optimizing the hits.
   
   

   

3. We have also applied FBDD for developing novel protein-protein interaction inhibitors of the p47phox subunit of NOX2. We screened our 2,500 fragments by fluorescence polarization (FP) and thermal shift assay (TSA) followed by surface plasmon resonance (SPR) validation. Biostructural studies by NMR and SAXS indicated that two fragments bound to two separate binding sites in the elongated conformation of p47phox, and the design of dimeric inhibitors thereby resulted in potent compounds (Solbak et al, 2020, J Med Chem). Since then, the compounds have been further optimized and tested in various biological assays (on-going). Recently, we assessed a literature compound suggested to target p47phox and inhibit NOX2. However, we found that the compound, LMH001, degraded within minutes in buffer and did not inhibit the p47phox/p22phox interaction (Zang et al, 2023, Front Pharmacol).
   
   
   

   

4. PDZ domains are intriguing but challenging drug targets. Recently, we investigated the druggability of PSD-95’s PDZ1-2 domain by fragment-based screening and a computational method. This resulted in new fragments shown to bind the PDZ domains of PSD-95 (Zang et al, 2020, ChemMedChem).

5. We are also engaged in many collaboration projects: For example, we have used SPR to characterize protein-protein interactions related to KDM5B (Dorosz et al, 2019, Sci Rep), NEMO (Jussupow et al, 2020, Sci Adv), and CaMKIIa (Leurs et al, 2021, PNAS USA). Also, we contributed with LC-MS pharmacokinetic data to a small-molecule obesity study (Grunddal et al, 2021, Mol Metab), and recently, we designed and synthesized novel Cas9 inhibitors by using a fragment-inspired deconstruction-reconstruction optimization strategy of a screening hit (Lee and Tran et al, 2022, J Med Chem).

Medicinal chemistry, SPR* and biochemical/biophysical assays are core methods of our group. X-ray crystallography is performed in close collaboration with internal colleague Prof. Michael Gajhede using various beamlines in Europe, e.g. ESRF (Grenoble), EMBL (Hamburg), MAX IV (Lund)**, and Diamond Light Source (Oxfordshire). NMR for studying ligand-protein interactions is done with collaborators in Germany (Helmholtz Zentrum München) and Denmark (Technical University of Denmark), and testing in cell assays and disease models by collaborators in Denmark (University of Copenhagen, University of Southern Denmark, Aarhus University), Sweden (Karolinska Institute), and USA (University of Miami).

- *See SelectScience interview about our Pioneer system and how we use it
- **See HALOS interview about X-ray experiments at MAXIV related to p67phox/NOX2

Recently, we joined UBIMOTIF – a Marie Sklodowska-Curie Innovative Training Network (MSC-ITN) – focusing on the ubiquitin system and E3 ligases and led by Prof. Jakob Nilsson; and initiated our collaborative project on TNF with Prof. Mads H. Clausen (Technical University of Denmark). (See our recent review here).

You can follow us on Twitter and Instagram (see also links in bottom of the page)

We thank the following foundations for their generous support of our research:

• Lundbeck Foundation (Fellowship and Ascending investigator grants)
• Independent Research Fund Denmark (Project 2 grant with Prof. Clausen)
• MSC-ITN (UBIMOTIF) (PhD stipend with Prof. Jakob Nilsson)
• BioInnovation Institute (BII) (Proof of concept grant)
• China Scholarship Council
• HALOS Cross Border Research Grant
• Torben and Alice Frimodt's Foundation
• Simon Spies Foundation
• Hørslev Foundation
• Augustinus Foundation

If you are you interested in doing a master thesis project in the group, please send your CV, grades and motivations to anders.bach@sund.ku.dk for further discussions. We have projects both within chemistry and biological areas of drug discovery.

- Examples of Master Thesis Projects:

1. Fragment-based drug discovery on protein-protein interactions (pdf)

2. Mechanism of action studies of p47phox inhibitors (pdf)

Currently we have no open PhD and postdoc positions in our group, but we are always interested in hearing from talented and potential candidates. If you are interested in becoming part of our group please send your CV and motivations to anders.bach@sund.ku.dk