Small, ‘drug-like’ molecules that bind selectively to ssRNA: don’t forget these papers

September, 2017

Thirty years ago, Noller (1987) used chemical footprinting to identify the positions at which several aminoglycosides bind to 16S ribosomal RNA.  Following papers by Schroeder (1991) and Green (1993), interest began to grow around the question:  Could folded ssRNA macromolecules be targets against which small, selective, ‘drug-like’ molecules would change their activity… as is currently the case for drug discovery aimed at protein targets?  If so, it would herald a “brave new world” for drug discovery with enormous potential.

The logical first step would be to see if a functionally-diverse set of aminoglycosides could target different RNA molecules.  Research was quickly carried out multiple laboratories; 21 Reviews of the resulting publications were published between 1999 and 2011, the most comprehensive as of that date being the Review by Thomas and Hergenrother (2008).  The discovery of riboswitches led to excitement about the potential of small molecule binders to affect biological activity (2002); a recent Review appeared in 2015.

I joined the BioOrganic group at Parke-Davis Pharmaceutical Company as Director in 1993.  As were several other labs, the group was determining the binding sites of aminoglycosides to TAR RNA.  To that date, the only drugs targeting RNA’s were the aminoglycoside antibiotics.  We made the decision to screen PD’s library of approx. 150,000 compounds to see if TAR could be a ‘druggable’ target.  We were in the unique position of having both a large compound library and the infrastructure to perform high-throughput screening, which enabled us to test this hypothesis.  The result of the screening was a surprise even to us.  We identified approx. 20 compounds that inhibited Tat-TAR association with therapeutic indices of TC50/IC50 ≥ 5 and selective for Tat-dependent transcription.  The group went on to identify which of these compounds functioned by binding to TAR.  Many of that set of 20 functioned in this way; cations, neutrals, and even anions.  We were given authorization to publish the structures of three; that paper was published in 1998.  A summary of the results in these two papers is provided on pages 2-4 of this document. Compound 3 on pg. 3 displays activity in vivo.

I am taking this unusual approach to re-kindling these results for two reasons:

1. All of the Reviews from 1999-2011 generously cited our group’s publications.  A much more recent (and excellent) Review, Connelly, Moon, and Schneekloth (2016), did not.  I contacted the Principal Author, who explained that the Review was intended to be an update to the 2008 Review by Thomas and Hergenrother.  This makes perfect sense.  In my opinion, the later Review will now be the ‘go-to’ publication that new researchers in this field use to learn what has been published previously.  Quoting the most recent Review, “Another challenge will be overcoming the problem of specificity and selectivity, which remains a major barrier for RNA-binding molecules.” The community needs to know selective TAR inhibitors can and have been discovered.  This fact will provide grant writers with a powerful argument for support of their work in this field.

2. It is important to me that the results of the leaders of this enormous effort- Dr. Houng-yau Mei and Dr. David Mack- receive the (admittedly delayed) recognition they deserve.  During that same period of time, the other half of our group was working on what became Combinatorial Chemistry, and received significant recognition for their work.  As Director, I was left in the position of assuring the RNA researchers that, “This area isn’t important today, but it will be important in the future.”  This has come to pass, actually earlier than the 20-year period between then and now.  I left Parke-Davis in 1996 and quickly lost track of the burgeoning RNA/small molecule field.  It was my responsibility to highlight the RNA team’s work, and I blew it; life got in the way.

I now take it as my responsibility to try and keep this work known to researchers in the field… especially academic researchers.  This is the best way I know how.  Thank you for taking the time to read this brief communication.

Anthony W. Czarnik