Regulation, biosynthesis and mode of action of formicamycins, promising new antibiotics with a high barrier to resistance

大多数用于医药的抗生素都是由土壤细菌链霉菌产生的天然产物制成的，链霉菌有数千种不同的菌株。它们是在1940年至1960年抗生素发现的黄金时期发现的。然而，到了20世纪60年代，科学家们开始重新发现相同的物种，制造出同样的已知化合物。他们放弃了寻找新的化合物，因为他们认为他们已经找到了所有的天然抗生素。事实上，他们只发现了容易找到的菌株和抗生素，即所谓的低挂果。2000年，随着细菌基因组测序，一切都改变了。基因组包含细胞生命的所有指令，通过阅读数以千计的链霉菌菌株的指令，我们现在知道这些细菌的指令比他们在实验室中制造的抗生素多得多。这意味着我们只在这些细菌的自然栖息地发现了一小部分由它们制造的抗生素。这是个好消息，因为我们必须发现和开发新的抗生素，以应对数量惊人的耐药感染。细菌可以迅速适应，对抗生素产生抗药性，这意味着我们之前发现的大多数抗生素不再起作用。这就是所谓的抗菌素耐药性(AMR)，英国政府预测，如果我们现在不能解决AMR问题，到本世纪50年代，我们将面临“抗生素末日”--抗生素将不再有效，传染病将成为比癌症更大的杀手，每年导致全球约1000万人死亡。已经提出了十个优先行动领域，包括提高公众意识和刺激早期抗生素发现，这两个领域都在我们的项目提案中。为了发现新的抗生素，我们使用基因组挖掘，这意味着对链霉菌基因组进行测序，然后寻找一系列指令(生物合成基因簇)来制造我们以前从未见过的新抗生素。我们发现并测序了生活在昆虫或植物根部的新的链霉菌菌株，我们操纵这些细菌来启动它们的抗生素的生产，例如通过对菌株进行基因工程来过度表达生物合成基因。我们之所以在这些环境中进行搜索，是因为它们以前被忽视了，而且有证据表明，来自这些环境的链霉菌菌株产生新抗生素的潜力增加。我们的研究还允许我们制造许多新的抗生素，这样我们就可以纯化它，确定它的活性，并找出它是如何杀死细菌的(目标和作用机制)。如果抗生素要被开发成药物，这些信息是必不可少的。了解产生细菌对抗生素的抗药性(为了避免自杀，必须如此)以及致病细菌是否容易获得抗药性也是至关重要的。易耐药的抗生素作为候选药物并不可取，但有时我们可以对其进行修饰，制造出更有效的半合成抗生素。我们利用基因组挖掘来鉴定一类新的抗生素，称为福尔卡霉素。它们对革兰氏阳性超级细菌(如MRSA和VRE)具有强大的活性，而且在实验室中它们不会对甲霉素产生抗药性。我们正在与一位合成化学家合作，制造更难杀死像大肠杆菌这样的革兰氏阴性细菌的新版本。我们还鉴定了生物合成基因簇，现在我们需要了解这些基因是如何调控的，并鉴定天然的抗性基因。我们将利用这一知识来改造菌株，使其在生物合成过程中过量生产福尔卡霉素和中间体。然后，我们将提纯大量分子进行半合成，并确定致病细菌的靶点、作用模式和抗药性。这些是确定他们是否是好的候选药物的关键的第一步。

Most of the antibiotics used in medicine are made from the natural products produced by soil bacteria called Streptomyces, of which there are thousands of different strains. They were discovered during a golden age of antibiotic discovery between 1940 and 1960. By the 1960s, however, scientists began to rediscover the same species, making the same, known compounds. They gave up searching for new compounds because they thought they had found all the natural antibiotics. In fact, they only discovered the easy to find strains and antibiotics, the so-called low hanging fruit.Everything changed in 2000 with the sequencing of bacterial genomes. A genome contains all the instructions for the life of the cell, and by reading the instructions for thousands of Streptomyces strains we now know these bacteria have instructions for many more antibiotics than they make in the lab. This means we have only discovered a small proportion of the antibiotics made by these bacteria in their natural habitats. This is good news because we must discover and develop new antibiotics to tackle an alarming number of drug resistant infections. Bacteria can adapt quickly and rapidly become resistant to antibiotics which means most of the antibiotics we previously discovered are no longer working. This is known as AntiMicrobial Resistance (AMR) and the UK government predicts that if we fail to tackle AMR now we will face 'Antibiotic Armageddon' by the 2050s - that antibiotics will no longer be effective and infectious diseases will become a bigger killer than cancer, causing around 10 million deaths worldwide every year. Ten priority areas of action have been suggested, including increasing public awareness and stimulating early stage antibiotic discover, both of which are covered by our project proposal.To discover new antibiotics, we use genome mining, which means sequencing Streptomyces genomes and then looking for sets of instructions (biosynthetic gene clusters) to make new antibiotics that we haven't seen before. We find and sequence new Streptomyces strains living on insects or in plant roots and we manipulate these bacteria to switch on production of their antibiotics, e.g. by genetically engineering the strains to over-express the biosynthetic genes. We are searching in these environments because they have been previously overlooked, and because there is evidence that Streptomyces strains from these environments have an increased potential for producing new antibiotics.Our research also allows us to make lots of any new antibiotic, so we can purify it, determine its activity and figure out how it kills bacteria (targets and mechanism of action). This information is essential if the antibiotics are to be developed as drugs. It is also essential to understand how the producing strain is resistant to the antibiotics (which it must be, to avoid suicide) and whether disease causing bacteria can acquire resistance easily. Antibiotics which are easily resisted are not desirable as drug candidates but sometimes we can modify them and make semi-synthetic antibiotics which are more effective.We used genome mining to identify a new group of antibiotics called formicamycins. They have powerful activity against Gram-positive superbugs like MRSA and VRE and they do not become resistant to formicamycins in the lab. We are working with a synthetic chemist to make new versions that target harder to kill Gram-negative bacteria like E. coli. We also identified the biosynthetic gene cluster and now we need to understand how the genes are regulated and to identify the natural resistance genes. We will use this knowledge to engineer strains to over-produce formicamycins and intermediates in its biosynthesis. Then we will purify large amounts of the molecules for semi-synthesis and to determine targets and modes of action and resistance in disease-causing bacteria. These are essential first steps in determining whether they are good drug candidates.