28 May 2018

Fragments vs the common cold (via NMT)

Anyone who has spent much time in drug discovery will have been asked what they've done to cure the common cold. In a paper just published in Nature Chemistry, Robert Solari, Edward Tate and collaborators from Imperial College London and institutions throughout the UK have taken a stab at this challenge.

One of the problems with rhinovirus, which causes the common cold, is that there are more than 100 different serotypes, thwarting vaccine development. To make matters worse, the virus replicates rapidly and sloppily, thereby increasing the odds of resistance mutations. To sidestep both problems, the researchers decided to target a host protein rather than a viral protein.

After the rhinovirus genome is translated in cells as a single polyprotein, it is cleaved and processed into component proteins which self-assemble to form the virion. One of the proteins, VP0, has a fatty acid attached to its N-terminus by host proteins called N-myristoyltransferases (NMT1 and NMT2 in humans). Mutagenesis studies had previously suggested that this modification is important for infectivity, so the researchers sought inhibitors against the NMTs.

High-throughput screens had previously identified two unrelated series of compounds, and crystallography revealed that they bind at adjacent but overlapping regions within the enzyme active site. Fragment-sized compound IMP-72 makes multiple interactions with the protein; an inhibitor from the other series makes a key interaction with an active-site serine. This molecule was trimmed back to a fragment (IMP-358) which showed minimal enzyme inhibition on its own but which dramatically increased the potency of IMP-72. Crystallography confirmed that the two fragments could bind NMT1 simultaneously.

A sort of fragment linking was conducted in which the key hydrogen bond acceptor of IMP-358 was attached to the more potent fragment, leading to a low nanomolar inhibitor. Further structure-guided optimization led to IMP-1088, which inhibits both human NMT1 and NMT2 with IC50 < 1 nM and shows picomolar binding by surface plasmon resonance (SPR).

So does it work? IMP-1088 is able to block myristoylation of VP0 in human cells. More importantly, the molecule shows antiviral activity against a range of rhinovirus serotypes and is able to rescue cells from viral cytotoxicity. Further mechanistic work suggests that inhibiting NMT activity blocks virus assembly.

Of course, lots of human proteins are myristoylated – NMT1 and NMT2 are human enzymes after all. Reassuringly, IMP-1088 itself did not reduce viability of uninfected cells. Although SPR had shown very slow off-rates, NMT proteins are constantly being resynthesized, and NMT activity had fully recovered after 24 hours. The researchers suggest that an early diagnosis and short treatment could be both safe and effective.

There is still much to do, notably pharmacokinetic and animal efficacy studies. And of course, the fear of toxicity will hang all the more heavily over antiviral strategies that target host proteins. So the next time someone asks whether scientists have invented a cure for the common cold, you’ll still have to tell them no. But at least we’re working on it.

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