How dirt can save humanity from an infectious apocalypse

No one has been combing Central Park in search of drugs the way Sean Brady does [ in American colloquial slang, drugs and drugs are indicated by one word drugs / approx. trans. ]. On a sweltering thursday, he jumps into a yellow taxi, crosses Fifth Avenue, and runs along a dirt path. We are surrounded by the all-pervading hooting of a helicopter, and the whistles of cars break through the trees. Brady, a fast-talking chemist far past 40 years old, with short cropped hair and rimless glasses, sarcastically and self-deprecatingly jokes about his extremely purposeful searches. He cuts circles tirelessly. Next to the lake, we head for a secluded place on a rocky slope. Brady leans over and picks up a pinch of dusty soil. “From this piece of soil,” he says, “enough material can be extracted for DNA analysis.” He holds the ground in his hand for a short time and then throws it away. The grains of glass quartz glisten in the sunlight.

Brady makes cures from mud. He is confident that the upper layers of the soil of our planet are incredible, inexhaustible sources of undiscovered antibiotics, chemical weapons that bacteria use to protect against other microorganisms. He is not the only one who thinks the same, but the problem is that most of the bacteria cannot be grown in the laboratory - and this is a necessary step in the cultivation of antibiotics.

Brady found a way to get around this restriction, opening the way to all these unused bacteria living in the mud. Cloning the DNA extracted from the mud soup and introducing these foreign gene sequences into microorganisms that can be grown in the laboratory, he developed a method for discovering antibiotics that could soon cure infectious diseases and fight against drug-resistant microorganisms. In early 2016, Brady discovered Lodo Therapeutics (lodo in Spanish and Portuguese means “dirt”) to scale up production and ultimately help humanity to overtake infectious diseases that come on our heels. Some colleagues call this approach a “walk in the park” [ idiom “a walk in the park” means a very easy solution to any problem / approx. trans. ]. Indeed, the lab recently sent two groups of student volunteers to collect dirt in bags at 275 different locations in New York.


Sean Brady is in search of ways to revive the antibiotic industry

We are back in their tracks back to the laboratory, advancing with shoes on the potential medicine for almost every conceivable disease. “That's amazing, really?” Says Brady, breathing hard. “Right here we can ... find ... all the medicines ... of the world. Its cool".

At that moment, when Brady and I are walking through Central Park, a 70-year-old woman is brought to the hospital in Reno, pc. Nevada, with an infection that no doctor can cure. A woman fell during a trip to India, and tissue fluid accumulated under her thigh. She flew back to the US, and then, after two weeks, died. A report by the US Centers for Disease Control and Prevention states that the microorganism that killed it could have survived when faced with 26 different antibiotics. The accused, Klebsiella pneumoniae , is not the only antibiotic-resistant microorganism that breaks through the protection of humanity - it belongs to the family of enterobacteria resistant to carbapenems . Carbapenems are the drugs of the last stage, and the Center for Disease Control and Prevention considers organisms that are not amenable to these drugs as "nightmares."

One of the problems with resistance to antibiotics is that for most people, this information remains rather abstract - there are relatively few lethal cases so far. Few of us have lost our loved ones in this way. Golden Hepherd methicillin-resistant Staphylococcus (MRSA) kills in the US 20,000 people a year, compared with 600,000 cancer victims. Therefore, it is rather difficult to imagine a future resembling the past when there were no antibiotics - the era of invincible staphylococcus , streptococcus , tuberculosis , leprosy , pneumonia , cholera , diphtheria , scarlet fever , puerperal fever , dysentery , typhoid , meningitis , gas gangrene and gonorrhea .

But it is precisely to this future that we are going. The daily use of antibiotics and the irresponsible handling of them accelerates the emergence of resistance to them in people and animals. We are rapidly moving back to the world where mortality begins in childhood, where premature babies die, where newborns are blind from gonorrhea. Ordinary injuries turn into life-threatening infections. You can lose a limb, or life, from careless handling of a knife to clean vegetables or from an accidental fall in India. The risks of organ transplants or medical implants will overpower any possible benefits. Make an ordinary visit to a dentist surgeon and end up in a body bag. Explosive virus epidemics like influenza are especially deadly if they develop in tandem with bacterial infections like streptococci. This epidemic does not threaten us - it is already among us, and it carries with it the end of medicine, as we knew it. That is why the search for Brady, aimed at the revival of discoveries of antibiotics, is so important.


Brady called on people from all over the world to send him the soil, and as a result he had a whole room of zip-bags of dirt.


Brady sometimes describes his work as some kind of archaeological excavation: he studies the remains of microbial civilizations.

Since 1939, when Rene Jules Dubot , a researcher at Rockefeller University, smeared dirt on a Petri dish and isolated the antibiotic gramicidin , the search for antibiotics was mainly tied to bacterial cultures and limited to the percentage of bacteria and fungi growing in the laboratory. And if the chance to find a new antibiotic in a random soil test was once estimated as 1 in 20,000, now this probability has decreased to one in a billion. All easy options have already been found.

Historically, this search is riddled with random discoveries. A strain of the fungi used to make penicillin appeared on moldy cantaloupe ; quinolones were found in a spoiled quinine lot; microbiologists first isolated bacitracin , a key ingredient of the Neosporin ointment, from an infected wound of a girl who fell under a truck. Other antibiotics have appeared in wild, remote places of the globe: cephalosporins came from sewers in Sardinia; erythromycin from the Philippines; Vancomycin from Borneo; rifampicin from the French Riviera; rapamycin from Easter Island. By persuading the microbes to grow under certain conditions, we dig for medical chemistry fighting our own microscopic enemies. But, despite the technical progress in robotics and chemical synthesis, researchers continued to rediscover many easily allocated antibiotics, because of which this “old school” method received an ironic nickname: “grind and find].

Therefore, Brady and others turned to metagenomics - the study of genetic information extracted from a certain environment. The technique appeared in the late 1980s, when microbiologists began to clone DNA directly from seawater and soil. Natural DNA, extracted and cut into pieces, can be worked in the laboratory by inserting fragments of foreign genes into bacteria such as E. coli, creating what is known as an “artificial chromosome.” These clones contain libraries, a living repository of all the genomes of all microbes found in certain places.

Using high- throughput DNA sequencing , scientists began to search these libraries, and their census produced such astronomical biodiversity that they began to add new branches to the tree of life. According to some estimates, over a trillion species of microbial organisms live on Earth. Up to 3000 species of bacteria can be contained in a single gram of soil, and each of them has four million basic DNA pairs wrapped around a single circular chromosome. The following steps were dictated by simple logic: find new genetic diversity, and find new chemical diversity.


In Lodo, ​​chemists extract and purify organic molecules, looking for new chemical structures, and perhaps the very only ideal molecule that can save millions of lives.

In 1998, Brady worked in a team that prepared a simple strategy for extracting DNA from microorganisms living in the mud, which involved mixing the dirt with a detergent, inserting gene fragments into E. coli, and reproducing clones in Petri dishes to see what they had done. By the time Brady set up his own laboratory at Rockefeller University in 2006, he had created quite a few new complex structures. Some had anti-cancer properties, others worked like antibiotics. He studied DNA caught from a tank in Costa Rica filled with bromeliads and created an antibiotic, palmitoylputrescine, an antibiotic that effectively coped in a test tube with resistant forms of hay sticks . Brady realized that he did not need to plow intact and remote ecosystems to study the biodiversity of the world. The necessary material for the creation of new drugs could be found much closer to home.

All this time, Brady has been watching how antibiotic resistance is ahead of a slowing series of discoveries. For the most part, the pharmaceutical industry is to blame. To conduct a new drug through clinical trials and test it in humans, it takes an average of 10 years and several billion dollars. At best, luck is one of the five drugs, so financial returns do not correspond to the tremendous value that antibiotics represent to society. Part of the blame lies in the nature and use of drugs: the more we use antibiotics, the less effective they become; the more selective pressure we apply, the more likely the emergence of resistant strains.

Therefore, antibiotics, such as carbapenems , used to treat the most deadly pathogens, are stored as extreme funds in the event that nothing else helps. Fatally ill patients take the last-line antibiotics, and either die or recover; in any case, they cannot be called regular customers, as a result of which the profit invested in the development of a means is negligible or negative. And to wait until the market for such vital antibiotics reaches a critical mass and becomes profitable is to be asking for a catastrophe. As Richard Ebright, a researcher at Rutgers University, explains: “Unfortunately, by that time you will receive 10 million people who will die in the next ten years while you are busy rebooting the system.” According to some estimates, antibiotics occupy only 1.5% of the development of new chemical compounds. According to the Pugh Charities, a non-profit organization, less than half of the drugs in development target high-priority pathogens, such as drug-resistant forms of staphylococcus and tuberculosis. And these are the most deadly diseases in the world, and they are at the top of the list of goals for Brady.


Bacteria multiply in liquid broth, a color that often resembles a chocolate drink, and the smell - fresh ground, like a newly dug pit


Lodo is founded with the goal of providing life-saving medicines to patients in the next 10-20 years.

Three years ago, Brady got a call from the Bill and Melinda Gates Foundation. On the line was Trevor Mandel, a former director of a pharmaceutical company, now serving in the foundation as president of world health. The foundation wants to look for drugs to treat tuberculosis, a disease that kills two million people a year, and overtakes AIDS in terms of death. Tuberculosis was once treated with a cocktail of three antibiotics, which includes rifampicin , or “reef”. It was discovered almost 50 years ago, and over time, the bacteria that cause tuberculosis developed resistance to it. Intrigued by Brady's approach, similar to science fiction, Mandel asked him if he could get a couple of new molecules that are effective against tuberculosis.

Brady is focused on finding analogues, minor tweaks, or modifications to the chemical structure of existing drugs. While searching in the metagenomic libraries created by Brady from soil samples, he could see in what different ways a reef appeared in nature. He was looking for a familiar pattern: clusters of genes that created something similar to the original reef molecule, only with a chemical bond in a slightly different place, or in an additional atom.

Find these analogues, and you will again be able to outwit Koch’s wand and effectively treat tuberculosis. In six months, Brady convincingly demonstrated that he is able to find reef analogues, as well as variants of antibiotics such as vancomycin and daptomycin , whose effectiveness also constantly decreases due to the emergence of resistance to bacteria in them. The foundation organized a business meeting for Brady and Bill Gates, and then, in January, receiving $ 17 million in investments from the Gates Foundation and the Accelerator investment fund from Seattle, Brady founded his company.

On a clear September day, Brady leads me to the Lodo office on the eighth floor of the glass tower of the Alexandria Center for the Sciences of Life Sciences . We pass a small room with a fridge and two incubators the size of a pizza oven that warms up flasks of bacteria, and he takes me to a clean laboratory with a view of Bellevue Hospital. Ten people work in Lodo. Eleven, if you count the robot. The PerkinElmer automatic workstation, which is large enough to allow a person to climb into it, speeds up the discovery process by searching the metagenomic libraries and fishing for clones containing the target sequence as if with an exact metal paw. The scope of work, which previously occupied the technologists and candidates of science from six months to a year, can now be completed in a week. And this speed is already justified. The table on the wall indicates about 30 potential antibiotics that the company is currently trying to create and describe - and this is the result of only one week. Recently, Brady found an antibiotic that cured methicillin-resistant Staphylococcus aureus (MRSA) in mice.

Brady walks around the robot with his hands in his pockets. The car is naughty, manipulators are still. The process begins with the soil sent by donors and volunteers. The Brady team processes the soil, reducing it to the DNA it contains, and clones fragments of the genes of organisms that cannot be cultivated, introducing them into bacteria, which are then stored in rectangular bricks the size of a brick — the so-called libraries. The difficulty lies in finding the target genes, since all the genetic fragments are mixed — it’s like someone leaving a box of thousands of puzzle pieces. “And we have such a huge mix,” says Brady, “and we start with 10 million clones and divide them into smaller sets.”


One gram of soil can contain 3,000 species of bacteria.

The Ludo bioinformatics team uses algorithms that predict which molecules are likely to come from which lab fragments, so the robot eventually restores those that contain gene clusters that are needed to create antibiotic molecules. The corners of Brady's mouth depict something like a smile. “There are many more steps in creating these things,” he says, “but this is exactly the kind of innovation that is happening here.”

Brady sometimes describes his work as some kind of archaeological excavation: he studies the remains of microbial civilizations, concentrates on how to use their genetic material to figure out how to reproduce a certain aspect of their community. “If you are looking for drugs,” he says, “you don’t need to know what is happening in the rest of society — how they built huts or canoes — if we say that antibiotics are weapons, then we only need information on weapons those genes where antibiotics are encoded, and then you need to take another step and build this antibiotic. ”

For this, a team of molecular biologists from Lodo manipulates DNA and grows clones in heated Erlenmeyer flasks . Bacteria multiply in liquid broth, a color that often resembles a chocolate drink, and the smell - fresh earth, like a newly dug pit. In the next room, chemists extract and purify organic molecules, looking for new chemical structures, and perhaps the very only ideal molecule that can save millions of lives.

Recently, researchers have tried to revive the area of ​​detection of new antibiotics in several ways. A team from Northeastern Boston University developed a special plastic chip that allows them to grow a wide variety of bacteria in the field, which led to the discovery of teixobactin in a meadow in Maine. Практически все соглашаются с тем, что обещаниям метагеномных поисков ещё только предстоит претвориться в жизнь. Как говорит Джилл Бэнфилд, биохимик из Калифорнийского университета в Беркли, пока применение этой технологии «сильно ограничено».

Warp Drive Bio из Кэмбриджа, шт. Массачусетс — одна из немногих компаний, использующих похожие технологии. Брэйди когда-то участвовал в её научном консультационном совете. Грег Вердин, сооснователь компании и химик из Гарварда, уверен, что нацеленная на ДНК «поисковая система геномов» выдаст новые антибиотики. «Если вы принесёте мне цветок в горшке, — говорит он, — я гарантирую, что смогу найти там новые антибиотики». Вердин фокусируется более узко и изучает существующие бактерии, подверженные культивации. Он считает, что клонируя ДНК некультивируемых бактерий, Брэйди вносит в и так сложную задачу «ненужные усложнения».

Несколько биотехнических фирм, первыми пытавшиеся использовать метагеномику для поиска новых лекарств, потерпели фиаско. «Эта большая идея носилась в воздухе, — говорит Джон Кларди, работавший советником у Брэйди, а теперь — в Гарварде. — Но я думаю, что Шон был первым человеком, доведшим идею до практического, пригодного к использованию применения». Кларди говорит, что одной из проблем остаётся систематическое предсказание того, какие гены содержат информацию о молекулах определённого действия. Иначе говоря, никто не знает, где в природе найти инструкцию по обезоруживанию смертельных инфекционных организмов. «Это очень узкое место, — говорит он. — У Шона есть идеи по поводу подходов, но они сильно отличаются от задач, которые он уже решал».

Брэйди садится в кресло в конференц-зале с видом на Ист-Ривер. Он признаёт, что никогда не думал о том, что ему удастся организовать компанию с офисом в элитарном здании на Манхэттене. В Alexandria Center, «большом модном здании», есть пивной бар и ресторан со знаменитым шефом. Брэйди считает, что работает на благо людей, и представляет собой чрезвычайно скромного парня, с несбыточной мечтой по организацию конвейеров, находящих новые лекарства, во всех странах мира. Он думает о том времени, когда устойчивые к антибиотикам штаммы переберутся из больниц в общественный транспорт — а с туберкулёзом это уже происходит. Lodo была основана с верой в возможность другого будущего, в котором через 10-20 лет пациенты смогут получить новые лекарства, спасающие жизни. Брэйди недавно огласил своё видение на регулярной встрече сотрудников: «Мы находимся здесь ни для чего более, кроме как для спасения жизней людей».

В сентябре Lodo разослала огромное количество электронных писем с текстом «Нам нужна ваша грязь». У Брэйди есть целая комната, заполненная мешками почти всех цветов радуги, полученными в результате призыва — серые, красноватые, тёмно-коричневые. Несколько лет назад он нанял скалолаза специально для добычи почвы. С тех пор сотни добровольцев набрали уже несколько литров земли в зиплок-пакетах. «Мы не намывам золото в ручье у вас во дворе, — говорит Брэйди. — Мы берём лишь немножечко почвы, которая вам всё равно не пригодится». Иначе говоря, ближайшая надежда человечества может оказаться заключённой в щепотке чего-то бесценного, и одновременно настолько же распространённого, как грязь.