This article is a preview from the Summer 2020 edition of New Humanist
Writing this in the midst of the Covid-19 crisis, I was struck by a curious fact of our technologically developed world. If we have caused global heating and spread plagues around the planet, it’s also true that we have – just in time – developed the technologies to mitigate these horrors. During the 14th-century plague, people huddled into churches to beseech God to end the affliction. Today we try to avoid such close physical contact – and we have the means to find vaccines and therapies to tackle any new plague. Developments that derive from our deep chemical knowledge of bacteria and viruses are revolutionising our approach to existential problems such as pandemics and the climate change crisis. The very creatures that cause our miseries are our key tools in the new biotechnology.
Bacteria are not just germs. Most are entirely benign, with functions in the environment that do not harm us. All of life’s fundamental processes were invented in bacteria. They had the Earth to themselves for around 2.5 billion years. But viruses are parasites. A virus like Covid-19 isn’t really alive – it is a geometric assemblage of DNA and proteins. The proteins latch on to receptor proteins in the human lung, gain entry, multiply mightily and do their damage. Within two weeks of the virus being recorded in China, its complete DNA sequence was posted online by Chinese scientists. In March, Science magazine published the crystal structure of the vital protein spike that the virus uses to enter the cell: a key target for a vaccine. Little synthetic strands of DNA are now being trialled for their ability to block the virus’s entry mechanism to human cells.
This deep knowledge of proteins enables scientists today to tweak nature in unprecedented ways, both to combat disease and to fashion a huge range of chemicals we need, without relying on the grossly polluting, energy-intensive industrial technologies we have used until now. The whole web of life is built from protein interactions – mostly life-giving and some, like those of Covid-19, malign. This is why the importance of protein engineering was recognised by the 2018 Nobel Prize for Chemistry, which was awarded to three pioneers of protein research.
Bacteria and viruses are virtuoso chemists, comprising a treasure trove of evolvable proteins that could, were we able to adapt them to our purposes, produce all the chemicals we need for energy, using artificial photosynthesis, as well as for plastics, pharmaceuticals, paints and glues. We can also use them to produce agricultural chemicals and cleaning materials, a high proportion of which are currently made from oil. Proteins are the real stuff of life. We’ve been led to believe that life is all about DNA. But in fact, DNA is mostly an inert keeper of the keys, out of action until coaxed back in by a bevy of catalytic protein helpers: enzyme nanomachines.
Not all proteins are enzymes. Your nails and hair are proteins but they’re just dead plastic, so to speak. Enzymes are the water-soluble, pulsing protein nanomachines of life. They carry out all the reactions in the living cell, each one of which is a nanoscale watery city – like a 3D Venice with teeming chemical routes worming their way through the cell in all directions. This might sound odd: cells are about a thousandth of a millimetre across. But the nano world is fantastically detailed at this very tiny scale. As the American theoretical physicist Richard Feynman memorably put it: “There’s plenty of room at the bottom.”
The enzymes, big knobbly molecules, have key active sites that only recognise a single chemical out of the thousands rushing past at any moment. So all the traffic proceeds in an orderly way. No need for traffic lights: the proteins are a smart system. It is enzymes that unzip DNA when it needs to divide to pass the genetic instructions to a daughter cell as an organism grows. It is enzymes that tap light from the sun to power the creation of plant biomass, and burn sugars to give us energy. All the processes of life are enzymatic.
For a long time, chemists and biologists could only admire and envy the power and precision of natural enzymes. But the 2018 Nobel Prize for Chemistry recognised the revolutionary possibilities of adapting bacterial enzymes for human use. Frances Arnold, one of the 2018 Nobel recipients, won it for revolutionary work that began by contemplating the great conundrum of proteins: there are potentially more of them than there are particles in the universe. Proteins consist of strings of 20 different amino acids in a precise order. The largest known protein, the vital human muscle protein titin, is 34,350 amino acids long. So proteins are like words with thousands of letters, very few of which are meaningful. Every semester, Arnold tells her students at the California Institute of Technology to read Jorge Luis Borges’ 1941 short story The Library of Babel, which imagines a library in which every conceivable book of 410 pages made of 25 characters is kept. The parallel isn’t quite exact, because the idea of looking for Hamlet in the Borgesian library is deliberately absurd, but thousands of real working proteins do exist out of the countless numbers of hypothetical proteins with no biological function. The notion of all possible proteins, in this Borgesian sense, is known as protein space.
What puzzled biologists about proteins is that with all this protein space to choose from, how does a protein happen to evolve to become a better protein? Arnold was inspired by the theorising of the influential biologist John Maynard Smith in a 1970 paper, in which he reasoned that for evolution to work, functional proteins – out of the myriad non-functional ones – must lie adjacent to each other in protein space. Nature has followed a trail, hopping across these stepping stones to produce the working enzymes we have today. Arnold determined to take steps through protein space that nature never attempted, in order to create proteins for human use in medicine and across the chemical industry.
Conventional chemistry is ingenious but enormously laborious. The great chemist Robert Woodward’s synthesis of the natural hormone cholesterol in 1951 took 39 stages, each intermediate being purified before entering into the next reaction. The real problems come when such processes are scaled up into huge chemical factories. These are dangerous places. In 1984, a facility in Bhopal, India, released a toxic cloud which killed at least 3,787 and injured over half a million.
Instead of all those elaborate rounds of individual reactions, Arnold’s process, known as directed evolution, takes natural bacterial proteins and subjects them to a process of artificial selection to be effective in reactions that she, not nature, chooses. This is similar to the way in which animal breeders artificially evolve new breeds of cattle, but rather than seeking more lean meat or milk, scientists select promising strains of bacteria for useful proteins for further evolution.
Directed evolution has already had a huge impact. It’s becoming the route of choice to create a range of chemicals, including environmentally friendly pesticides and pharmaceuticals, detergents, low-carbon chemicals and fuels from plant carbohydrates. Directed evolution represents a great act of healing, in which we gently tweak nature’s processes using these new enzymatic techniques.
This may sound a roundabout route, but we can’t simply design and synthesise proteins – because we don’t know what protein structure will give us what we need. And neither does nature. Evolution lights upon better functional proteins by chance and so does Arnold. She sets out to generate as many variants of an enzyme as possible, then screens them for the activity she was searching for. Enzymes are adaptable and often have very minor functions besides their main ones. Nature’s enzymes, in the hands of a chemist like Arnold, can evolve new functions because, to some degree, they already possess them. By screening successive generations, the minor activity can be boosted to become a major one.
Arnold has founded two start-ups to move her technique into commercial production. Gevo, founded in 2005, makes biofuel and is exploring renewable bioplastic bottles, flavours and fragrances, as well as bio-based industrial chemicals. Provivi, founded in 2013, makes an engineered version of insect pheromones to reduce the use of dangerous pesticides. Big commercial players are also using these techniques – for example, to reduce the need for polluting artificial fertilisers.
But the triumph of directed evolution can best be seen in recent work by the US pharmaceutical company Merck. Islatravir is an experimental drug under development to treat Aids. In trials, it has achieved rapid suppression of the virus. The drug was first created using conventional chemistry, but the Merck team wanted to find a method that used evolved enzymes. This would reduce the temperature at which reactions take place, thus simplifying the process and avoiding the multiple steps required by conventional chemistry. The ingenuity of the Merck team’s approach is staggering. Using nine enzymes – all acting in one reaction – the new process results in an excellent 51 per cent overall yield of islatravir.
Directed evolution isn’t just another useful technique. It is revolutionary and visionary on several counts. Evolution is the greatest puzzle. When nature makes great leaps in evolution, it doesn’t do so by “inventing” a new gene; it finds a new, often totally different, use for an old one. For around 2 billion years, life consisted of single-celled organisms. The genes involved in controlling the interactions between cells in multicellular creatures like human beings were already there in rudimentary form in single-celled creatures. Genes are like Swiss army knives, ready to undertake all kinds of tasks if necessary.
The 2018 Nobel Prize for Chemistry also went to George Smith and Greg Winter for their work in developing phage display. Just as we are now seeking a molecule that recognises the proteins of Covid-19 and disables them, phage display seeks proteins that can bind to a molecule of interest. Phage display is very similar to directed evolution in its goals, but has developed along different lines. In Winter’s work, that molecule of interest was the gruesomely named tumour necrosis factor (TNF), which kills cancer cells but is also a causative factor in many auto-immune diseases. To find a molecule that could bind to TNF, and stop it from causing auto-immune damage, many bacteria infected by variant phages are swilled over a plate coated with TNF. If a bacterium has a protein that binds to the TNF, it will be retained when the others are washed off. The binding efficiency is then enhanced by going back to evolve further variants of the phage that is already capable of binding to some degree. This screening technique is sometimes called “panning”. The echo of gold dust in that word is apt because Winter’s work created what is currently the best-selling pharmaceutical in the world: Humira (adalimumab), with sales of over $18 billion in 2017.
Phages (which I wrote about in the Spring 2019 New Humanist) are a kind of virus that preys on bacteria. And it’s the interactions between phages and bacteria that lie behind their human usefulness. For most of the time that these tiny organisms – bacteria and viruses – have been known to science (still only just over 150 years for bacteria, around 120 for viruses) they have been seen mostly as a threat to human wellbeing, which they indeed can be. But they could also be our way out of environmental and health crises. A get-out-of-jail-free card of sorts.
That is because our detailed knowledge of the interactions between bacteria and viruses is our key to solving the killer diseases. If our struggle with Covid-19 and other scourges is equivalent to a world war, the new frontline is situated in this nanoworld of organisms, which are neither intrinsically good nor bad, but must be understood in context. Bacteria are also helping to create a sustainable, nature-inspired chemistry to bring our human materials and energy production back within a benign natural ambit. This will allow us to have the life-support systems we need without trashing the planet, replacing oil-based energy and chemical production with Arnold’s directed evolution.
In her 2018 Nobel Prize address, Arnold said: “Life – the biological world – is the greatest chemist and evolution is her design process.” The new chemistry is part of the necessary movement towards working with nature instead of against it. The ability to work with enzymes – nature’s engines – is a vital but so far under-recognised strand of the green revolution. Solar power and wind farms are forms of material engineering, but the crisis is in the natural world. The macro environment is only the sum of myriad interactions at the nano level: in other words, proteins. We’re now learning nature’s ways – and just in time.
