The small molecule PF-06446846 selectively blocked the translation of PCSK9 messenger RNA, showing that the ribosome can be targeted in a protein-specific manner.

Researchers from the University of California Berkeley and Pfizer Inc. reported the findings in the March 21, 2017, online issue of PLoS Biology.

"Generally, we think about small molecules that target the ribosome and protein synthesis as shutting down and perturbing the production of most proteins," co-corresponding author Jamie Cate told BioWorld Today. Cate is a professor of molecular and cell biology and of chemistry at UC Berkeley, and a faculty scientist at Lawrence Berkeley National Laboratory.

Such nonspecific inhibition is the mechanism of antibiotics such as erythromycin. Antibiotics also target the bacterial ribosome rather than the human one.

Translarna (ataluren, PTC Therapeutics Inc.), which has been conditionally approved by the EMA for the treatment of Duchenne's muscular dystrophy, targets the human ribosome, but its mechanism is in some ways the opposite. Rather than stalling translation, it works by having the ribosome read through a premature stop codon.

By contrast, PF-06446846 "only seems to block the translation of a very small subset of the human proteome. . . . With the method we used, we could only detect about 20 or so," he said. "I still think it's amazing."

PF-06446846 itself is not slated for clinical development. A Pfizer spokesperson said that the molecule "represented an early lead compound for the oral PCSK9i program which did not enter clinical development. Separately, Pfizer evaluated two distinct clinical candidates for the oral PCSK9 program that have been discontinued. The rationale to discontinue development of these small molecules does not reflect our continued interest toward exploring the potential of this exciting new mechanism for the treatment of disease."

PCSK9 inhibitors as a class have been clinically successful but commercially disappointing to date. (See BioWorld Today, Nov. 2, 2016.)

Late last year, Pfizer halted development of its PCSK9-targeting antibody, bococizumab, which had reached phase III. (See BioWorld Today, Nov. 2, 2016.)

According to the company, however, "the decision to discontinue the bococizumab global development program is unrelated to any ongoing work involving these small molecules."

Beyond the specifics of PCSK9, the work opens up a new targeting mechanism – although for now, there are more questions than answers about how broadly useful the approach will turn out to be.

PF-06446846 interacts with both the ribosome and the beginning part of the protein, and the sequences where the interactions are occurring are "very short," Cate said.

As a net result, translation of the protein stalls as it is coming through the ribosome.

What is still unclear is why PCSK9 and a few other proteins are susceptible to stalling, while most are not.

"We still can't use the protein primary structure – we can't just look at it and say 'Oh, this will be a stalling sequence,'" Cate said. "There are some unifying features, but . . . there's a lot we don't understand."

Co-corresponding author Robert Dullea, senior principal scientist at New York-based Pfizer, said that one of the current avenues of research focuses on understanding the structural interaction among the drug, the protein and the ribosome.

"Understanding those mechanisms and really probing further at the ribosome may help us understand a bit more why the mechanism appears to be so selective," Dullea told BioWorld Today.

The team also plans to investigate the cellular consequences of halting PCSK9 translation. In the work now published in PLoS Biology, treating rodents with PF-06446846 led to a drop in plasma PCSK9, total cholesterol and low-density lipoprotein (LDL), or "bad" cholesterol. "In this first paper, we focused really on the very first steps," Cate said. At this stage, all we know is a more global view. What happens between stalling and protein drop – we are still working on understanding that."

Another goal is to find additional compounds that stall translation of different proteins. "Now that this has been established, the hope is that one could apply the methodology to other targets," Dullea said.

Spiros Laris, vice president of medicinal chemistry at Pfizer, told BioWorld Today that one advantage of PF-06446846 is that "it is really a different molecule compared to the products that have been used as antibiotics,"

Antibiotics are natural products, and are extremely complicated to synthesize – so much so that they are "the center of much academic research in total synthesis," Laris sad. "People can make their name if they come up with a more efficient synthesis of those compounds."

In comparison, PF-06446846 is relatively simple to synthesize, which will make exploring the chemical space around it that much easier.

"These [ribosome inhibiting processes] may not be limited to those chemical classes, and that in itself is worth interrogating," Laris said. "Our hope is that these properties are not unique to this motif."