Structure-Based Drug Design
The unique pulse structure of the LCLS allows structures of drug targets to be solved at room temperature with minimal radiation damage, resulting in unprecedented insights into drug-binding pockets.
Understanding structure-based drug design
The function of a biological object can be inferred from its structure. Knowledge of the structure is used for developing new drug targets. For example, if the structure of the protein shows a cluster of exposed amino acids with high electronegativity, then the designed drug should be the appropriate size and shape and have an appropriately exposed grouping of positive amino acids that will bind in the pocket. Drugs are designed using the ‘Lock and Key’ principle: if the shape of the lock (protein) is known, the proper key (drug) can be designed to activate it.
Inaccurate structural information of the blue pin lengths prevents the black key's design (on the left) from effectively positioning the blue pins and allowing the yellow tumbler to rotate. When accurate structural information of the blue pin lengths is available, this allows the gray key (on the right) to effectively rotate the yellow tumbler. Figure obtained from Wikimedia Commons.
Current issues to overcome
To achieve such knowledge about the structure of the targeted substrate, a high level of accuracy is needed. Ideally, Ångstrom-level resolution—enough detail to see small bond lengths—is sought. Many drug targets are therefore studied at the synchrotron light source, which provides the X-rays required to observe such fine details using X-ray diffraction.
However, to slow down the effects of X-ray absorption and the resulting radiation damage to the biological object, cryogenic cooling is used. Measuring X-ray diffraction under non-physiological temperatures can severely bias the structure and obscure protein side chain mobility in the drug-binding pocket.
How LCLS can help
What makes the LCLS a powerful tool for structural-based drug design is that the X-ray photons are delivered in a short pulse. This brilliant flash of energy destroys the sample, but it gives a view of the undamaged structure before the X-ray radiation damage begins to propagate.
As a result, structures can be measured at ambient temperature with minimal radiation damage. Dynamics between the protein and drug are important for interaction and binding, and ambient temperature structures will offer more biologically relevant electron density maps. With the fidelity of the structure determined at the LCLS, more precise drug targets can now be designed.
Structure-based drug design at LCLS through the years
Shining light on sleeping sickness
One of the first cases leveraging the LCLS was the room-temperature 2.1 Å resolution structure of a fully glycosylated precursor complex of cysteine protease Cathepsin B (TbCatB) from the parasite Trypanosoma brucei. This enzyme is involved in host protein degradation in African sleeping sickness.
Researchers needed more detailed information about the parasite's enzyme structure to design a drug that attacks only the parasite and not a very similar enzyme in humans. The room temperature TbCatB structure obtained at the LCLS was the highest resolution structure at the time, which enabled the design of new treatments.
When angiotensin hormones bind to the angiotensin G-protein coupled receptor (GPCR), the corresponding G-protein signals the constriction of blood vessels leading to a higher blood pressure. Blocking the binding of angiotensin hormones with a drug, such as with an angiotensin receptor blocker (ABR), can lead to lower blood pressure. Unfortunately, blocking the angiotensin receptor also blocks the beneficial actions of other GPCRs, which for example help to prevent dizziness.
Using the LCLS, the room temperature structure of the angiotensin II type 1 receptor (AT1R) when bound to a specific ABR could be determined, allowing the portions of the ABR which were critical to binding to be identified. Previous drug designs were equivalent to pulling fuses into your home to turn off a hot desk lamp. With the new information from LCLS, a better ABR can be designed that will block the negative effects of hypertension while allowing the positive benefits to continue.
Now, instead of pulling the fuses in your home and cutting off all the lights, including the hot desk lamp, a new technique, such as a cooler lower wattage bulb can be employed, while still being able to use the other benefits of electricity throughout your home.
Furthermore, the team continued to develop their understanding of drug targets for hypertension by elucidating the binding pocket of the seemingly similar, AT2R. Typically, the similar pockets imply that similar drugs would be effective; however, this was not the case in clinical studies. Drugs that were successful in treating issues related to AT1R were not nearly as successful as in treating those related to AT2R.
Binding pocket of AT1R on the left, AT2R on the right.
The room temperature AT1R and AT2R structures determined using the LCLS showed an unexpected result: although AT1R and AT2R can sometimes bind the same compound, their drug-binding pocket show clear differences. With this structural information, drugs can be designed that are specific for the AT1R or AT2R pocket and scientists no longer have to rely on an educated guess of what the drug-binding pocket looks like. This finding demonstrates the power of the LCLS in the field of structure-based drug discovery.
The war with bacteria: fighting the resistance
One way to defeat a bacterial infection is by targeting the transcription center of the bacteria’s ribosomes, hindering its ability to build new proteins. In 2015, the DeMirci group used the LCLS to image the 30S small subunit of the bacterial ribosome from Thermus thermophilus bound to the paromomycin antibiotic. The room temperature data revealed significant differences in the global structure of the small subunit and the conformation of the antibiotic compared to the cryogenic structure.
After the structural insights into the antibiotic effect of paromomycin were published, researchers in the Ricci group reached out to the DeMirci and coworkers to use the capabilities of LCLS to study the room temperature structure of the 30S subunit bound to other antibiotics, such as sisomicin and a newly designed derivative, N1MS. In this way, LCLS can help researchers develop more effective antibiotics to better fight bacterial infections.
Hasan DeMirci explains more about the structural biology of ribosomes and the action of antibiotics in the following SLAC Public Lecture:
Next to studying how antibiotics can inhibit bacterial machinery, the LCLS has been used to analyze the room temperature structure of bacterial enzymes such as β-lactamase, which inactivate antibiotics. This helps researchers design new, better drug candidates that are impervious to enzymatic attack.
The following publications highlight how LCLS has advanced other areas of structure-based drug design in the past few years:
- Liu et al. (2021) Molecular basis for lipid recognition by the prostaglandin D2 receptor CRTH2. Proc Natl Acad Sci USA 118: e2102813118.
- Stauch et al. (2019) Structural insights into melatonin receptors. FEBS J 287: 1496-1510.
- Luginina et al. (2019) Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs. Sci Adv 5: eaax2518.
- Ischenko et al. (2019) Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCrJ 6: 1106-1119.
- Johansson et al. (2019) XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. Nature 569: 289-292.
- Stauch et al. (2019) Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature 569: 284-288.
- Clairfeuille et al. (2020) Structure of the essential inner membrane lipopolysaccharide–PbgA complex. Nature 584: 479-483.
- Durdagi et al. (2021) Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Structure 29: 1382-1396.
- Ciftci et al. (2021) Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein. Sci Rep 11: 15819.
- Ciftci et al. (2019) Serial femtosecond X-ray diffraction of HIV-1 Gag MA-IP6 microcrystals at ambient temperature. Int J Mol Sci 20: 1675.
- Zook et al. (2020) XFEL and NMR Structures of Francisella lipoprotein reveal conformational space of drug target against tularemia. Structure 28: 540-547.