Jerry’s Favs from the Recent OTS Meeting

  • 12th Annual OTS Meeting in Montreal Très Excitant!
  • RNAi Approach to Treating Preeclampsia Spurred by Researchers’ Personal Experiences
  • Ionis Video for Spinal Muscular Atrophy Amazes the Audience
  • 30 years later, PS-Modified Oligonucleotides Continue to be Enabling!
montreal

City line of Montreal. Taken from oligotherapeutics.org

The 12th Annual Meeting of the Oligonucleotide Therapeutics Society (OTS) held on September 25-28, 2016 in French-speaking Montreal, Quebec, Canada brought together hundreds of enthusiastic investigators from around the world. All attendees share a common interest in oligo-based therapeutics, and we gratefully say merci beaucoup to the organizers of this very well run event.

Commenting here on my “favs” is limited by space, and highly subjective—by intent—focusing on only several impressions that struck me as worth sharing. Readers interested in perusing all of the lecture titles and speaker biosketches can do so at this link, which also lists corporate sponsors—including TriLink—and connects with the regularly updated OTS website.

Jerry’s balcony view of OTS 2016 presentations at the Centre Mont-Royal venue

Jerry’s balcony view of OTS 2016 presentations at the Centre Mont-Royal venue

Before getting to my selected topics, I wish to congratulate the OTS Board of Directors and Scientific Advisory Council for their ongoing valuable contributions to this society, and continuing efforts to include participation by the new generation of young investigators, who I’m sure will collectively make exciting advances in the field of oligonucleotide therapeutics. It was pleasure for me to me meet some of these “next gen” scientists, and learn about their current work, which is quite sophisticated by comparison to what I and others did in the early—dare I say primitive—era of antisense oligonucleotide drug discovery.

Toward Treating Preeclampsia: Personalized Drug Developers’ Stories

Preeclampsia (PE) is a disorder that occurs during pregnancy, affects both the mother and the fetus, and is characterized by elevated blood pressure, swelling and protein in the urine. According to a Preeclampsia Foundation fact sheet, every minute somewhere in the world a woman dies in pregnancy or childbirth, which amounts to more than 500,000 deaths each year. In addition, PE causes ~15% of premature births in industrialized countries and is the number one reason doctors decide to deliver a baby early.

Dr. Melissa J. Moore is a professor in the RNA Therapeutics Institute and the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School. Taken from hhmi.org

Dr. Melissa J. Moore is a professor in the RNA Therapeutics Institute and the Department of Biochemistry and Molecular Pharmacology at the University of Massachusetts Medical School. Taken from hhmi.org

In her OTS lecture on clinical development of an RNA interference (RNAi) approach to treat PE, Dr. Melissa J. Moore (pictured below) introduced an attention-grabbing personal element when she revealed her bout with PE. Coincidentally, she discovered that her then attending physician, Dr. S. Ananth Karumanchi, had begun his quest for identifying PE-causality at the molecular level prompted by his daughter’s dangerously premature birth due to PE. This turned out to be a truncated kinase receptor abbreviated sFlt1, which Moore described as Karumanchi’s break-through discovery for possible development of PE therapeutics.

The condensed version of these two remarkably interwoven, PE-related personal stories—that you can hear first-hand from Moore on YouTube—was an agreement between Moore and Karumanchi to collaborate on discovering whether double-stranded short-interfering RNA (siRNA) targeting sFlt1 could be useful as an RNAi-based PE therapeutic agent.

Melissa Moore’s ultrasound sonogram. Taken from her YouTube video

Melissa Moore’s ultrasound sonogram. Taken from her YouTube video

Moore went on to gratefully acknowledge her colleague at the RNA Therapeutics Institute, Prof. Anastasia Khvorova, for setting up “by hook or by crook” the first non-profit academic facility for large-scale production of siRNA suitable for clinical development. This led to designing and producing a nuclease-resistant siRNA comprised of 2’-OMe/2’-F ribonuceosides and phosphorothioates at the ends, with an attached hydrophobic cholesterol moiety for improved delivery.

Even more impressive—at least to me—was Moore’s ability to access pregnant baboons in a non-human primate model of PE. This is inherently difficult due to issues involving non-human primates for any research, and is technically much more challenging compared to, for example, infectious disease models. Dr. Moore showed lots of compelling results from her model studies, and concluded her talk by saying that clinical studies were planned.

In closing this section, it’s worth noting that Moderna—a leading mRNA therapeutics company—has recently announced its appointment of Dr. Moore as Chief Scientific Officer of Moderna’s mRNA Research Platform.

Ionis Pharmaceuticals Drug Video for Spinal Muscular Atrophy Amazes the Audience

Dr. Stanley T. Crooke. Taken from ionispharma.com

Dr. Stanley T. Crooke. Taken from ionispharma.com

This year’s OTS Lifetime Achievement Award address by Dr. Stanley T. Crooke, founder and CEO of Ionis Phamaceuticals (formerly Isis Pharmaceuticals), was presented to an auditorium packed with attendees who, like me, greatly admire Crooke’s many scientific and commercial contributions to the field over the past decades. These currently include more than 450 (!) scientific publications and 38 drugs in the pipeline, with 3 finishing Phase III—very impressive and promising indeed!

Ionis’ impact on providing efficacious oligonucleotide-based therapies to patients was conveyed most powerfully—in my opinion—by a video about Cameron, an infant SMA patient who was born with Spinal Muscular Atrophy (SMA). According to an NIH fact sheet, SMA is a genetic disease that causes weakness and wasting of the voluntary muscles in the arms and legs of infants and children. These disorders are linked to an abnormal or missing gene known as the survival motor neuron gene 1 (SMN1), without which motor neurons in the spinal cord degenerate and die.

As detailed elsewhere by Chiriboga et al., Nusinersen (aka ISIS-SMNRx or ISIS 396443) is a 2’-O-(2-methoxyethyl) (MOE) phosphorothioate-modified antisense oligonucleotide (ASO) designed to alter splicing of SMN2 mRNA and increase the amount of functional SMN protein produced, thus compensating for the genetic defect in the SMN1 gene. The cartoon shown below depicts how this ASO targets an hnRNP-A1/A2–dependent splicing silencer in intron 7 of the SMN pre-mRNA. Nusinersen displaces hnRNP proteins from this silencer site on the SMN2 pre-mRNA, facilitating accurate splicing of SMN2 transcripts (e.g., increasing the synthesis of transcripts containing exon 7) and resulting in increased production of full-length SMN protein.

Taken from researchgate.org after Chiriboga et al.

Taken from researchgate.org after Chiriboga et al.

Ionis and its commercial partner Biogen announced in August 2016 that Nusinersen met the primary endpoint pre-specified for the interim analysis of ENDEAR, the Phase 3 trial evaluating Nusinersen in infantile-onset (Type 1) SMA. The analysis found that infants receiving Nusinersen experienced a statistically significant improvement in the achievement of motor milestones compared to those who did not receive treatment. In September, Biogen announced that it applied for Priority Review by the FDA that, if granted, would shorten the review period of Nusinersen following the Agency’s acceptance of the NDA filing by Ionis and Biogen.

Cameron at 2+ years enjoying the moment with his mom. Taken from YouTube

Cameron at 2+ years enjoying the moment with his mom. Taken from YouTube

The amazing effect of Nusinersen warranting this Priority Review is best appreciated—in my opinion—by watching a YouTube video showing the progress of Cameron during his treatment. When viewing this video, keep in mind that Cameron’s Type I SMA is typically evident at birth or within the first few months, and that symptoms include floppy limbs and trunk, feeble movements of the arms and legs, swallowing and feeding difficulties, and impaired breathing. Sadly, the prognosis is poor for babies with SMA Type I. Most die within the first two years. But not so for Cameron, shown below at 2+ years, thanks to Nusinersen!

Phosphorothioate-Modified Oligonucleotides Continue to be Enabling—30 Years On!

men

Left: Prof. Fritz Eckstein. Taken from oligotherapeutics.org Right: Prof. Wojciech J. Stec. Taken from cbmm.lodz.pl

That nuclease-resistant phosphorothioate (PS)-modified internucleotide linkages have had an enabling influence on all manner of oligo-based drug development is evident from the first-ever OTS Lifetime Achievement Award in 2015 being given to Prof. Fritz Eckstein for his pioneering and life-long work on PS linkages in DNA and RNA. Following Fritz’s lead, and aided by the availability of ABI’s DNA synthesizer, Prof. Wojciech J. Stec and yours truly published the first completely automated method for synthesis of fully or partially PS-modified DNA oligos in 1984. This opened the door for early antisense experiments with PS-modified oligos, which have continued now for 30 years!

Perhaps surprisingly, the ever evolving field of oligonucleotide therapeutics continues to rely on PS-modifications in a myriad of mechanistically distinct strategies, such as “classic” antisense to mRNA, siRNA, anti-miRNAs, modulators of RNA splicing, etc. In this regard, Dr. Crooke’s concluding remarks on his goal of deciphering the “code” for protein binding to chemically modified ASO, led me to muse about the negatively charged P-Smoiety in such binding of PS-containing ASO.

Taken from zon.trilinkbiotech.com

Taken from zon.trilinkbiotech.com

My initial thought was that P-S likely enhances binding to positively charged amino acid moieties in proteins, due to greater polarizability vs. P-O, and that Sp or Rp P-Sstereochemistry may likely influence binding. Moreover, this spatial aspect of a binding “code” can now be studied using stereospecific synthesis of PS-ASO by either Stec’s OTP method or Wada’s oxazaphospholidine method. Time will tell—stay tuned!
As usual, your comments here are welcomed.

Highlights of 2015 Publications Using TriLink BioTechnologies Products

  • Publications Citing TriLink Products Exceed 6,000
  • TriLink Products Showed up at a Rate of One Publication per Work Day
  • Among These Customer Publications, Modified mRNA is Trending
Taken from thetrymovement.com

Taken from thetrymovement.com

From my college classes decades ago, I can still clearly recall—thankfully—many “ah ha” moments. Most importantly is when I crystalized to purity and then confirmed structure by NMR the first compound I synthesized in Organic Chemistry Lab. Another ah ha moment—but on a completely different level—was during a philosophy class when the professor partially paraphrased a quote by Aristotle as “we are what we do.” The full quote given above is even more thought provoking because it ties in the notion of excellence, which I took to heart then, and have attempted to live by ever since.

Continue reading

Reflections on Advances in Medicinal Oligonucleotides

  • Oligos Are Not “Magic Bullets”
  • Oligos Have, Nevertheless, Enabled New Drug Paradigms
  • Oligos Continue to Attract Significant Corporate Investments

Reflections

The 10th Annual Meeting of the Oligonucelotide Therapeutics Society (OTS) is in full swing today in San Diego, CA where it began on Oct 12 and concludes on Oct 15. Having worked on antisense oligos since the early days (~30 years ago) participating in this meeting led me to several thoughts that I wish to share with you in this post.

First of all, contrary to many sceptics in those early days, the concept of using synthetic oligonucleotides as an entirely new class of medicinal agents has not only survived but also greatly expanded in terms of the biological target/mechanism of action and types of oligo constructs used—each with a seemingly endless array of chemical modifications to evaluate. In approximate chronological order of discovery, these targets and the types of oligos they have now come to include are listed below coincidentally, most of these are represented in the 2014 OTS agenda.

Target
mRNA
dsDNA
transcription factors
immunostimulation
proteins
splice junctions
RNA interference
Oligo Type
antisense
triplex
dsDNA decoys
CpG
aptamers
blockers
siRNA

 

 

 

 

 

Secondly, while it has been possible for oligo chemists to design and synthesize a plethora of modified oligos to achieve optimized nuclease stability, binding to target, etc., efficient delivery has remained the single most challenging problem to deal with. In talks on medicinal oligos, this situation is oftentimes eluded to as something to the effect of “there are only three remaining problems to solve: delivery, delivery, and delivery.”

Lastly, contrary to early hopes of being Dr. Ehrlich’s “magic bullets” (see caption below), oligos didn’t quite prove to be the new paradigm for a speedy concept-to-clinic solution. As all of us in the oligo world know, oligo-based therapeutics have encountered long and costly R&D timelines and clinical development paths typical of all other classes of therapeutic compounds.

Continue reading

Hot Topic in Oligonucleotide Therapeutics: Nanomedicine

  • What is it?
  • Why is it Hot?
  • How do Nucleic Acids Fit in?

The upcoming Oligonucleotide Therapeutics Society (OTS) annual meeting on Oct 12-15 in San Diego has an agenda with a number of presentations that could each qualify as a hot topic to highlight in this blog post. While mulling over which to pick, the talk by Prof. Weihong Tan—an extraordinarily prolific researcher at the University of Florida—entitled DNA-based molecular medicine and nanomedicine triggered my decision to comment on nanomedicine because it’s at the nexus of multiple scientific disciplines and various aspects of medicine.

Continue reading

30 Years of Automated Amidite DNA Oligos and Going Strong

Is this the most enabling biotechnology yet? I think so, what do you think?

A list of Historical Events for 1983 includes Michael Jackson’s “Thriller” album going to #1 and airing the final TV episode of “M*A*S*H” watched by a record 125 million viewers. Aside from this pop culture, 1983 was quite remarkable in the history of biotechnology. Two closely interconnected and unquestionably transformative events occurred: introduction of automated synthesis of DNA oligonucleotides (aka oligos) by Applied Biosystems, Inc. (ABI) and invention of PCR by Kary Mullis. My July 15th post gave scientific homage, if you will, to the enabling power of PCR and ended by noting that ready access to synthetic DNA oligos was, in effect, “enabling the enabler” and likewise deserves comment here.

Picks and shovels for the biotechnology gold rush

In recently published reflections entitled The Chemical Synthesis of DNA/RNA: Our Gift to Science, Prof. Marvin H. Caruthers gives a firsthand account of the initial development of the now well-known phosphoramidite (amidite) method for oligo synthesis with members of his research group at the University of Colorado at Boulder, notably, Serge Beaucage, Mark Matteucci, Bill Efcavitch, Curt Becker, and Lincoln McBride.

marvin

Prof. Marvin H. Caruthers, 2006 National Medal of Science Laureate (Bing Images).

These reflections go onto a very interesting backstory on founding ABI in Foster City, California to commercialize automated oligo synthesis using solid-phase amidite methodology, as pictured below. This, together with automated protein sequencers, peptide synthesizers, and related “tools”, were envisaged as enabling the then emerging field of biotechnology.

solidphase

Automated solid-phase phosphoramidite DNA oligonucleotide synthesis cycle (adapted from M. H. Caruthers, J. Biol. Chem. 2013, 288: 1420-1427).

ABI’s co-founder and first CEO, Sam Eletr, metaphorically referred to ABI’s tool-provider business model as making the “picks and shovels for the biotechnology gold rush.” Bill Efcavitch, Curt Becker, and Lincoln McBride joined ABI to do this, while Serge Beaucage went to Beckman (which introduced its amidite-based DNA oligo synthesizer shortly after ABI), and Mark Matteucci joined Genentech to do oligo synthesis. For further background on the history of this revolutionary technology, click here for a 1983 publication by Köster and coworkers on β-cyanoethyl (CE) phosphoramidites in oligo synthesis.

andre

Mr. Andre Marion (left) and Dr. Sam Eletr (right), who co-founded ABI in 1980 (Bing Images) as a company that would manufacture and sell “picks and shovels for the biotechnology gold rush,” are still very active in commercial biotechnology.

Transforming targeted drug development with antisense therapeutics

My small part in this story involved being chosen as one of the early-access test sites for ABI’s first amidite-based oligo synthesizer (while at FDA/NIH), and then joining ABI in 1986 to commercialize new applications. These applications included automated amidite RNA oligo synthesis and scale-up (1umol → 10umol →200umol) of DNA oligos.  We focused on modified oligos as potential antisense inhibitors of mRNA function, particularly methylphosphonate (PCH3) and phosphorothioate (PS) oligos, which at the time were gaining scientific attention—and new venture investments—as the “next big thing” for targeted drug development.

Continuing the historical evolution and impact of the commercialization of oligo synthesis…Lynx Therapeutics was subsequently spun-out of ABI in 1992 to pursue antisense therapeutics.  Today, this field is led by Isis Pharmaceuticals.  It’s been a few years now and these applications are indeed proving to be the next big thing, as demonstrated by ISIS’s recent announcement of FDA approval of KYNAMRO™ (mipomersen sodium or ISIS 301012) for the treatment of homozygous familial hypercholesterolemia.

kynamro

In this announcement, Stanley T. Crooke, MD, PhD, Chairman of the Board and CEO of Isis said that “KYNAMRO™ is the first systemic antisense drug to reach the market and is the culmination of two decades of work to create a new, more efficient drug technology platform.” The structure of ISIS 301012 is reported to be a hybrid RNA/DNA/RNA 20-mer that is fully PS-modified, and has five 2′-O-(2-methoxyethyl)-modified (2′-MOE) ribonucleosides at the 5′ and 3′ ends, ten 2′-deoxynucleosides in between; all cytosines are methylated at the C5 position: 5′-GCCTCAGTCTGCTTCGCACC-3′. PS and 2’-MOE modifications provide resistance to degradation by nucleases, while the central DNA segment allows RNase H-mediated cleavage of the mRNA target.

Congratulations to Dr. Crooke and to Isis for this milestone achievement for amidite chemistry! With over 25 other oligo drugs under active development in Phase 2 or higher, we expect to see the FDA approving more of these types of drugs in the near future. Click here for a survey and summary of these oligo drugs.

Stunning scalability:  billion-fold batch-size and million-fold parallelism

ABI’s original synthesis-scale for automated amidite DNA oligo assembly was 1umol, which was soon followed by 10umol and then 200umol batch-sizes. Far greater scalability was driven by the need for ever increasing amounts of oligos in preclinical animal experiments and subsequent clinical studies. Eventually, oligo drug commercialization required further investment in cost-effective process development. When I asked Dr. Yogesh Sanghvi, (formerly with Isis and founder/President of Rasayan, Inc.) about batch-size for oligo drug manufacturing, he said that “oligo synthesis scale has been increased to 750mmol using a solid-support method.“ Click here for his review of the current status of synthesis, chemical modifications, purification, and analysis of modified oligos for therapeutics.

By contrast to these very large single batch-sizes for manufacturing of an individual oligo drug, conventional gene synthesis and, especially, emerging applications in synthetic biology, require very small batch-sizes for manufacturing many thousands of different oligos. One way this has been achieved is through the use of multi-well plates for parallelized solid-phase synthesis of thousands of oligos at a time. Such approaches make “pennies per base” cost to customers a reality. If one assumes that ~1nmol and ~1mol single-batch scales are technically “doable,” then the scalability for solid-phase amidite synthesis is ~109-fold!

Fundamentally different strategies for producing huge numbers of tiny amounts of oligos employ massively parallelized array-based amidite synthesis, unblocking and cleavage from the array, and then either single-tube multiplex manipulations or use of water/oil picoliter-sized droplets.

Enabling never ending and expanding scope of science and technology

In this blog, I’ve explored the use of oligos in targeted drug development and the amazing diversity of manufacturing scales for oligos. These versatile enablers have also played—and continue to play—transformative roles in countless other areas of science and technology. Being a bit “PowerPoint-challenged” and squeezed for time, I opted for simply listing below various types of science and technology enabled in part by automated amidite DNA (and RNA) oligo synthesis. This list is not ordered in any way and it is not intended to be comprehensive, but it is quite an impressive list, nonetheless. There’s strong “entanglement,” so to speak, between DNA oligo synthesis and seemingly indispensable PCR (and other) amplification methods. Consequently, many of the listed items are “co-enabled” by oligo synthesis and amplification. Links to representative literature or websites are provided for readers who may be interested in more information.

Oligo synthesis: quo vadis?

There’s absolutely no doubt in my mind that currently available automated amidite oligo chain-assembly will continue to enable significant expansion of major nucleic acid-based applications beyond the types listed below. It’s less clear to me whether a non-amidite method will be invented to replace amidite chain-assembly for some applications and/or enable new applications for which amidite methodology is inadequate. Other chemical and/or enzymatic processes are conceivable, and there are likely some very creative minds musing over possible ways to outperform amidites relative to “faster, better, cheaper” oligo production, so never say never.

Comment on this list or any other content herein is welcomed.

List of science and technology enabled by oligos:  

sanofi

Sanofi’s newly launched facility for large-scale production of semi-synthetic artemisinin, a potent anti-malarial represents a further milestone in an anti-malarial drug partnership led by OneWorld Health, a non-profit drug development organisation, with funding from the Bill & Melinda Gates Foundation. Sanofi plans to have 60 tons per year capacity in 2014, which would meet at least a third of the annual global need for the drug (taken from European Biotechnology News via Bing Images). Click here for more on this facility and here for a 2013 Nature publication of the science.

triangles

DNA origami triangles, self-assembled in a single step from over 200 DNA strands. Each is a single 5 megadalton molecular complex, incorporating 15,000 nucleotides. ~120nm per edge, 1µm scan. Sample courtesy of Paul W.K. Rothemund, California Institute of Technology (taken from Asylum Research via Bing Images).

 

algae

Biodiesel can be made from algae; click here for advantages of using algae for biofuel production (taken from our-energy.com via Bing Images).