Science Pool

The NADase SARM1 (sterile alpha and TIR motif containing 1) is a key executioner of axon degeneration and there is great interest in developing SARM1 enzyme inhibitors as candidate therapies for multiple neurodegenerative diseases.

Through a combined approach of X-ray crystallography and cryo-EM we uncovered the molecular mechanism of SARM1 inhibition by a compound (DSRM-3716), demonstrating that it undergoes a base-exchange reaction with the nicotinamide moiety of NAD+, and that the transferase product is the bona fide inhibitor. Further more we reveal the activated state of SARM1 for the first time.

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Huntington´s Disease (HD) is a hereditary neurodegenerative disorder that is caused by a mutation in the huntingtin gene (mHTT) leading to deposition of pathologic protein aggregates in the brain.

This paper focuses on:

• Visualization of mHTT aggregate expression by positron emission tomography (PET) in rodent HD model
• Utility of the previously described novel PET imaging ligand CHDI-180 for detection of mHTT in rodent and post-mortem human HD brain
• Ability of CHDI-180 to serve as functional response indicator for mHTT lowering therapies

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SARM1 is a NADase whose action triggers the destruction of axons and development of novel SARM1 inhibitors which enables the prevention or delay of neurodegenerative disorders. This paper identifies the binding site for the SARM1 agonist NMN and reveals the structure of full-length SARM1 as elucidated by cryo-electron microscopy (cryo-EM). The structure of apo SARM1 was revealed as an octameric ring, held in an autoinhibitory state by the separation of the active TIR domain at the rim of the ring. The elucidation of autoinhibition release and the identification of the NMN binding site within the autoinhibitory ARM domain opens a path to inhibition of SARM1 via stabilisation of its inactive form. These studies were possible through the close co-ordination of the new cryo-EM team at Evotec, Abingdon with Disarm and academic collaborators in Australia and the USA.

Proposed SARM1 activation mechanism:

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Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, kills 1.5 to 1.7 million people every year. Macrophages are Mtb’s main host cells and their inflammatory response is an essential component of the host defense against Mtb. However, Mtb is able to circumvent the macrophages’ defenses by triggering an inappropriate inflammatory response. Understanding macrophage interactions with Mtb is crucial to develop strategies to control tuberculosis. The present study aims to determine the inflammatory response transcriptome and miRNome of human macrophages infected with the virulent H37Rv Mtb strain, to identify macrophage genetic networks specifically modulated by Mtb virulence.

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N-Methyl-D-aspartate receptors (NMDARs) are members of the ionotropic glutamate receptor family and play a crucial role in learning and memory by regulating synaptic plasticity. Activation of NMDARs containing GluN2A, one of the NMDAR subunits, has been recently identified as a promising therapeutic approach for neuropsychiatric diseases such as schizophrenia, depression, and epilepsy.

Identification of a new hit for GluN2A PAMs is however difficult due to the similarity of PAM binding sites between GluN2A and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPARs), another member of the ionotropic glutamate receptor family.

In this collaborative publication with Takeda, we focus on:

• Identification of an hit compound with moderate AMPAR-binding activity, though a Ca²⁺ influx-based high throughput screening campaign with a compound set including an internal AMPAR-focused compound library
• The strategy using a structure-based drug design (SBDD) approach to minimize the AMPAR-binding activity while improving GluN2A activity
• The use of the potent and brain-penetrable GluN2A-selective positive allosteric modulators GluN2A PAM discovered as in vivo tool exhibiting significant neuroplastic enhancement in the rat hippocampus 24h after oral administration, having potential application for cognitive enhancement in neuropsychiatric diseases

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This article published in Nature describes a first-in-class METTL3 inhibitor for the treatment of acute Myeloid Leukaemia.

The publication covers:

• Development of STM2457 following high-throughput screen
• Selectivity screening across the panel of 45 human methyltransferases
• Crystal structure of METTL3-14 complex with STM2457, part of structure-based drug design strategy for this target
• Compound validation in cellular assays and in vivo efficacy

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Alastair Parkes, Ph.D, Group Leader, Discovery Chemistry, Evotec UK

As part of our ongoing efforts at Evotec to tackle AMR through the design of novel antibiotics we have been working with Boston-based X-Biotix in a collaboration focussed on targeting priority Gram-negative pathogens. We are now able to share the story of our work on inhibitors of UDP-N-Acetylglucosamine Acyltransferase (LpxA), a key enzyme in the biosynthetic pathway of the outer membrane lipopolysaccharide of Gram-negative bacteria. Building on hit-finding work at X-Biotix we put together a multi-disciplinary team including Medicinal Chemistry, Computational Chemistry, Structural Biology and DMPK at our Abingdon UK site, in vitro and in vivo Microbiology and PK at our Alderley Park UK site, and in vitro Biology at our site in Hamburg, Germany. Through structure and property-based optimisation we were able to design highly potent inhibitors of Pseudomonas aeruginosa LpxA that were active against multi-drug resistant clinical isolates. To our knowledge, this is the first reported LpxA inhibitor series with selective activity against P. aeruginosa bacteria. In our paper in the Journal of Medicinal Chemistry we share the optimisation story, along with a significant quantity of activity data that we hope will be useful for other teams working on small molecule strategies to tackle P. aeruginosa and other Gram-negative bacteria.

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The ‘core’ metabolome of the Bacteroidetes genus Chitinophaga was recently discovered to consist of only seven metabolites. A structural relationship in terms of shared lipid moieties among four of them was postulated. Here, structure elucidation and characterization via ultra-high resolution mass spectrometry (UHR-MS) and nuclear magnetic resonance (NMR) spectroscopy of those four lipids (two lipoamino acids (LAAs), two lysophosphatidylethanolamines (LPEs)), as well as several other undescribed LAAs and N-acyl amino acids (NAAAs), identified during isolation were carried out. 

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Alastair Parkes, Ph.D, Group Leader, Discovery Chemistry, Evotec UK

The problems surrounding the economics of antibacterial drug development are well known, with the cost of simply keeping a product available for use now outstripping revenues from sales in many cases.

However, early R&D push incentives from organisations such as CARB-X and the new AMR Action Fund are keeping research going, while efforts continue to try to ensure the true value of novel antibiotics are recognised, spearheaded by the UK’s pilot of a subscription model for reimbursement of developers of new antibiotics

The challenges of running clinical trials sufficient for approval and securing adequate sales returns can affect scientific strategy, resulting in the targeting of only broad-spectrum agents most desired by clinicians. Through years of research, and discussions with members of the antibacterial research community, it became clear to me that the understandable focus on what both regulators and the market will currently support can be at odds with some of the most promising avenues in the science of antibacterial drug discovery. Narrow spectrum or even single pathogen agents may be of huge value in years to come, and from a scientific perspective, these compounds may be more readily accessible than broad-spectrum drugs.

As a medicinal chemist, my primary focus is on molecular design, and while there are many excellent reviews in the field, I felt that a perspective addressing how the many aspects of antibacterial drug discovery affect our design strategies would be a useful addition. I visualise any problems from the viewpoint of the antibiotic molecule, and consider the various challenges it must overcome to become a useful agent for clearing bacterial infections. In each case I consider how our knowledge should influence design strategies. While these principles are at the heart of our research at Evotec, I hope that sharing these ideas with the wider community will aid researchers in their work to address the growing threat of AMR.

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