Molecule of the Month: Capturing Beta-Lactamase in Action

Around 75% of antibiotics in use today are based on β-lactams, a group that includes penicillins, cephalosporins, and carbapenems, and which all include a characteristic 4-membered lactam ring. These antibiotics are effective because they resemble the natural substrates of proteins responsible for remodeling bacterial cell walls. When cell wall enzymes bind to β-lactam-based drugs, it blocks them from binding their normal substrates, halting cell wall formation and ultimately leading to cell death. However, bacteria have developed resistance through a family of proteins called β-lactamases, which work by binding to β-lactam-based molecules and cleaving the lactam ring, rendering the antibiotics ineffective.

To design better drugs, it is essential to understand how β-lactamases work. This is challenging, however, because the cleavage reaction occurs very rapidly and is difficult to capture using standard structural techniques. In X-ray crystallography, crystallized proteins are exposed to X-ray beams to capture a diffraction pattern, which can be used to determine molecular structures. These X-rays tend to be continuous and of relatively low-intensity, allowing a crystal to be exposed to the X-ray beam for an extended period of time while data is collected. A newer technique, serial femtosecond crystallography (SFX), utilizes X-ray free-electron lasers (XFELs) to deliver short, intense X-ray pulses to samples, capturing diffraction patterns just before the samples are destroyed.

Small crystals can be used for SFX, enabling researchers to rapidly introduce small chemicals (such as antibiotics) to the protein crystals in specially designed diffusive mixers. These small molecules can then diffuse into the protein crystals and trigger a reaction. Using this new method, called mix-and-inject-serial-crystallography (MISC), a reaction can be observed at high resolution by injecting the crystal mixture into the XFEL beam at different times after mixing.

In 2018, researchers designed a MISC experiment to see if they could capture the action of a β-lactamase at an XFEL source. In this experiment, tiny protein crystals of the Mycobacterium tuberculosis β-lactamase BlaC were mixed with the antibiotic ceftriaxone just before exposure to X-ray pulses. Data collected at 30 milliseconds, 100 milliseconds, 500 milliseconds, and 2 seconds after mixing revealed that the cleavage reaction primarily occurs between 100 and 500 milliseconds. The reaction involves a nucleophilic attack by a β-lactamase serine, which opens the β-lactam ring and forms a covalently-bonded intermediate before the β-lactam is hydrolyzed and released. Within 2 seconds, the enzyme has already bound to a new antibiotic. As shown on the right, BlaC crystallizes as a tetramer (6B68) made up of four copies of the enzyme. Interestingly, only two of the four enzymes were observed to catalyze the cleavage reaction during the course of the experiment.

Mix-and-inject serial crystallography has also been used to study inhibition of β-lactamases by so-called suicide substrate inhibitors, which irreversibly bind to β-lactamases and block their activity. Inhibition of BlaC by one such drug, called sulbactam, was recently studied. As shown on the left, the process of inhibition begins with the formation of a noncovalent enzyme-inhibitor complex in the active site (30 ms, 8EBR). Mirroring the reaction with ceftriaxone, this is followed by a nucleophilic attack by the catalytically active serine. In this case, however, this results in a covalently bound acyl-enzyme intermediate which renders the enzyme inactive (240 ms, 8EC4). Sulbactam, which is smaller in size than antibiotics like ceftriaxone, was observed in the active site of all four BlaC subunits. In the two light blue subunits, however, the reaction occurs so quickly that a pre-catalyzed sulbactam substrate was not observed. In the dark blue subunits, the reaction proceeded slowly enough for researchers to observe sulbactam binding before catalysis. Sulbactam and similar inhibitors have been approved by the United States Food and Drug Administration for use in fixed-dose combinations with previously approved β-lactam antibiotics (e.g. sulbactam plus ampicillin, know as unasyn).