An enzyme in bacteria known as histidine kinase is a potential focus for new types of antibiotics. However, it has been challenging to create drugs that target this enzyme due to the fact that it is a “hydrophobic” protein that loses its structure when it is taken out of its usual place in the cell membrane.
A team led by MIT has now discovered a method to render the enzyme soluble in water. This discovery could potentially enable the rapid screening of potential antibiotics that could disrupt its functions.
The researchers developed a new version of histidine kinase by making changes to four hydrophobic amino acids and replacing them with three hydrophilic ones. Despite this major alteration, the water-soluble form of the enzyme still maintained its original functions. Since there are currently no antibiotics that target histidine kinase, drugs that can interfere with its functions could potentially serve as a new type of antibiotics. This is particularly important in light of the increasing issue of antibiotic resistance, which results in over 1 million deaths annually.Shuguang Zhang, a principal research scientist from the MIT Media Lab and a senior author of the study, emphasized the significance of the protein as a potential target for drug development due to its uniqueness to bacteria and absence in humans. The study, co-authored by Ping Xu and Fei Tao, both professors at Shanghai Jiao Tong University, and Mengke Li, a graduate student at the same university and former visiting student at MIT, was published in Nature Communications. This protein, which is vital for cell functions, presents a promising opportunity for new drug development.The proteins are embedded in the cell membrane, with hydrophobic segments that allow them to associate with the membrane’s lipids. However, when these proteins are removed from the membrane, they tend to lose their structure, making it challenging to study or screen for drugs that might interfere with them.
In 2018, Zhang and his colleagues developed a simple method to convert these proteins into water-soluble versions that maintain their structure in water. This technique, known as the QTY code, uses the hydrophilic amino acids th
Leucine (L), isoleucine (I), and valine (V) are transformed into glutamine (Q), threonine (T), and tyrosine (Y) when they are incorporated into proteins.
Subsequently, the researchers have applied this method to a range of hydrophobic proteins, such as antibodies, cytokine receptors, and transporters. These transporters include a protein utilized by cancer cells to expel chemotherapy drugs from the cells, as well as transporters that brain cells employ to move dopamine and serotonin into or out of cells.
In the latest study, the team aimed to illustrate, for the first time, that the QTY code could be utilized.The objective was to design enzymes that are water-soluble and maintain their enzymatic activity. The study concentrated on histidine kinase due to its potential as a target for antibiotics. Most existing antibiotics function by harming bacterial cell walls or disrupting the production of ribosomes, which are responsible for protein synthesis. Histidine kinase is not targeted by any of these antibiotics, yet it is a crucial bacterial protein that controls processes like antibiotic resistance and cell-to-cell communication. Histidine kinase has the ability to carry out four distinct functions, such as phosphorylation – the process of activating other proteins by adding a phosphate group to them.
Human cells have a protein called histidine kinase which plays a role in transferring a phosphate group to histidine residues. This process is known as phosphorylation. On the other hand, dephosphorylation involves the removal of phosphates from histidine residues. While human cells also have kinases, they target different amino acids compared to histidine. As a result, drugs that inhibit histidine kinase would not affect human cells.
Following the conversion of histidine kinase to a water-soluble form using the QTY code, the researchers assessed all four of its functions and confirmed that the protein retained its ability to perform them. Consequently, this protein could be utilized in high-throughput screens to quickly evaluate whether potential drug compounds disrupt any of these functions.
A stable structure</p rnrnUsing AlphaFold, an artificial intelligence program, the researchers created a structure for a new protein and used molecular dynamics simulations to analyze its interaction with water. Their findings revealed that the protein forms strong hydrogen bonds with water, contributing to its structural stability.
Furthermore, the researchers discovered that simply replacing the buried hydrophobic amino acids in the transmembrane segment was insufficient to maintain the protein’s function. It was necessary to replace the hydrophobic amino acids across the entire transmembrane segment in order to preserve the molecule’s structural integrity.Zhang is now considering applying this technique to methane monooxygenase, an enzyme in bacteria that can change methane into methanol. A water-soluble form of this enzyme could be sprayed in areas where methane is released, such as cow barns or thawing permafrost, to help reduce methane levels in the atmosphere, a greenhouse gas. “If we can use the QTY code tool on methane monooxygenase and utilize the enzyme to convert methane to methanol, we could potentially slow down climate change,” Zhang explains. This study was supported in part by the National Natural Science Foundation.The Establishment of China’s Foundation.
