Reinventing Oligonucleotide Synthesis

 Wow, where to begin,

Our latest endeavors on the P(V) front are now published in Science. Now, before talking about the research, I must begin by giving a shout out upfront the (rather large) team who is responsible for everything in the paper. It was an incredible collaboration and everyone had a crucial role to play.

 

Bristol Myers Squibb: Yazhong Huang, Shenjie Qiu, Bin Zheng, Stephen Mercer, Richard Olson, Mike Schmidt, Ivar McDonald and Martin Eastgate

TSRI: Wei Hao, Julien Vantourout, Natalia Padial, Javier Lopez, Rohan Narayan, Donna Blackmond  and Phil Baran

After the team’s initial work developing the PSI reagents for the stereocontrolled synthesis of phosphorothioate linkages, much work remained to build out the P(V) platform, both to include other types of desired P-linkages but also to develop a protocol for using the novel reagents on an automated oligo synthesizer. The development of these additional reagents PS2, PO and RacPS all proceeded in different ways.

The challenges overcome in the syntheses of the PS2 and RacPS reagents were a simpler story so I'll direct you to finding that info in the publication. On the other hand, there is the P(O) reagent. To the best of our knowledge there had never been a published P(V) reagent capable of forming a phosphodiester bond between two nucleosides with phosphoramidite-like kinetics (i.e. crazy quick). The initial hit for such a reagent came in July of 2018, followed by my famous last words: “shouldn’t take long to find the perfect P(O) reagent” Although the hit was exciting, it required KOtBu as a base and wasn’t compatable with DBU or organic bases that would be amendable to an automated oligo synthesizer. 

To address this, we evaluated new P(O) reagents on several criteria:

1. Could they be made (Synthesis)

2. Could they be reacted with a nucleoside to afford a monomer (Loading)

3. Could they be coupled via an organic base with a second nucleoside to afford a dinucleotide  (Coupling)

We had two ways of making the reagents, either synthesizing 1,3-mercaptopropanols and reacting them with POCl₃ or by generating analogous compounds with 1,3-diols and PSCl₃ followed by an interesting atom transposition using TBAI. We found a lot of things that could work (and plenty that couldn’t) but only one scaffold was able to accomplish all 3 of our goals. P(O)-5 the diphenyl scaffold.  After this discovery we investigated the aryl electronics and stereochemistry of the diphenyl backbone. Attempts to modulate the coupling efficiency through the aryl electronics proved negligible. 

The stereochemistry was a more interesting questions, because the first synthesis of this reagent used a racemic mixture of the mercaptopropanol, generating a racemic mixture of P(O) reagents which upon loading onto a chiral nucleoside revealed a mixture of the possible isomers that one could imagine. We began synthesizing single isomer versions of these reagents and observed that the Syn scaffold epimerized into an inactive form during the loading step. 

Further investigation of the anti-backbone revealed that the (R,R) substituted system gave the fastest coupling times. We next looked into the synthesis of this reagent, the stereochemistry could be programed in via a Noyori reduction and using PFP as a leaving group provided suitable physical properties to afford a solid reagent. Despite this success, the reagent still had two flaws, it wasn’t stable enough (could only survive about a week on the benchtop) and it was still a mixture of isomers, with one reacting much faster than the other. 

Sitting around the lab one day, we thought to ourselves, why don’t start with the original PSI (a reagent we knew reacted at lighting speed) and swap the S for O? It seemed rather straightforward. In practice we were never able to do this successfully on the PSI reagent itself so we tried it on the PSI loaded monomers instead. Although we could succesfuly perform S-O transpositions on these monomers, there were always side reactions associated with the transformation, ultimately leading us to abandon this approach. 

Third times a charm as they always say, so revisiting the idea of performing the S-O transposition on the reagent itself, we knew we the reagent formed with PFTP (PSI) was too reactive after making the P(O) version of itself. So after generating PSI alternatives with different leaving groups, we found that we could successfully perform this transposition to generate a stable reagent, most notably the 4-bromothiphenol version.

There’s plenty more to the story. We evaluated the kinetics of the P(V) molecules, demonstrating that they are on par with phosphoramidite chemistry, we developed a novel universal linker capable of performing oligo synthesis under the unusual basic conditions found in the P(V) protocol and we even took a trip to Cambridge MA to visit our collaborators at BMS and see and learn first-hand how they were making oligonucleotides.

Also, if you’ve read this far it’s fair to assume you’re a fan of the P(V) approach to oligos so check out our perspective on P(V) chemistry that was also just published in ACS Central Science!

 

If you’re still reading, and want to follow the next steps of the P(V) story, keep an eye out on Elsiebio.com or drop one of us a line to check out how were using the P(V) technology (among other things) to develop the next generation of oligonucleotide therapeutics and “replace dogma with data”.  – Kyle and the P(V) Team

IKA GUEST POST ON CLASSIC ALTERNATING CURRENT MODE

ELECTRASYN 2.0 SOFTWARE UPDATE TO SUPPORT ALTERNATING POLARITY IN CONSTANT VOLTAGE REACTION MODE 

Author information:

Chuanjun Jiao, IKA Works, Inc. 3550 General Atomics Court, MS G02/321, San Diego, CA 92121-1122, United States

Email: charles.jiao@ika.net

 

Note: This report is not related to the recently added new function “Rapid Alternating Polarity (rAP)”. The change described here is relevant only when the default “alternating polarity” function is used together with a reference electrode. Currently, only “alternating polarity” function is supported to be used with a reference electrode, and rAP function is not compatible with a reference electrode.  In addition, further software update is not necessary to a unit in which the rAP function is already installed, since the latest software supporting the rAP function already includes this change.  

Background

 

Recently the Reid Group at University of Strathclyde reported a mechanistic study of electrochemical benzylic oxidation with the use of ElectraSyn 2.0 (ChemElectroChem 2020, 7, 2771). During their study, the group observed unexpected product distribution change when alternating polarity was applied during a constant voltage experiment with ElectraSyn 2.0. The report describes their careful investigation of this phenomenon, and casts a practical consideration on users of IKA ElectraSyn 2.0.  

Here is the key points of their report:

 

·       Unexpected outcome was obtained under the condition of constant potential reaction mode­– reference electrode ON–alternating polarity ON.

·       During alternating polarity, the same magnitude of current would be expected in both positive and negative phase. However, the observed current magnitude was totally different between these two phases.

·       This asymmetric current distribution affected electrochemical reaction, resulting in unexpected product selectivity change.

·       Therefore, ElectraSyn 2.0 might have an engineering concern.   

Summary of IKA investigation

 

IKA conducted a series of experiments to clarify the nature of this phenomenon and to improve ElectraSyn 2.0. The detail of our internal investigation can be found in Detail of our investigation in this document. Here we would like to provide a summary of our investigation. 

·       We verified asymmetric current distribution in the same setting described in the report (constant voltage–reference electrode ON–alternating polarity ON).

·       This asymmetric current distribution was observed only when reference electrode is ON. In other words, this issue does not occur when reference electrode is OFF. 

·       This is simply originated from how voltage is controlled in ElectraSyn 2.0. 

·       Accordingly, ElectraSyn 2.0 does not have engineering concern.

 

Software update

Although we confirmed that ElecraSyn2.0 does not have any engineering flaw, we updated ElectraSyn 2.0 software to enable equal current distribution in the above experimental conditions (constant voltage–reference electrode ON–alternating polarity ON). 

When this setting change is needed

 

A user needs to enable this function only when Constant Voltage reaction mode with Reference Electrode ON and Alternating Polarity ON  

 

Effect on past research 

 

The issue only occurs when Constant Voltage reaction mode with Reference Electrode ON and Alternating Polarity ON. In other conditions, current and voltage control is accurate and experimental data is reliable.

Detail of our investigation 

 

IKA ElectraSyn 2.0 provides many functions that satisfy different requirements for electrosynthesis. Among those functions, Constant Voltage is a reaction mode where the reaction is executed at a fixed voltage. This reaction mode is generally more selective than Constant Current mode, though the reaction time tends to be longer. Alternating Polarity is an option that periodically switches anode and cathode. This option is useful when electrode fouling is observed. Switching polarity helps to alleviate accumulation of deposit. Both Constant Voltage and Alternating Polarity are routinely used for electrosynthesis. 

 

The recent report by the Reid group described a mechanistic study in synthetic organic electrochemical method development with the use of ElectraSyn 2.0 (ChemElectroChem 2020, 7, 2771). In this report, unexpected product selectivity change was observed in electrochemical benzylic C–H oxidation of toluene derivatives by employing Constant Voltage alongside Alternating Polarity function equipped in ElectraSyn 2.0.

 

During those experiments, it was observed that the magnitude of the current during the second half of alternating period was greater than during the first half; giving an asymmetric current over time response. This is not desired because alternating polarity is simply an electrode cleaning technique and should not alter the magnitude of current.

Further in-depth investigation of cell potential with alternating polarity revealed that the voltage during the negative phase was not controlled. The set voltage was 1.5V, which means the reaction voltage should alternate between 1.5V and -1.5V. However, the observed voltage was clearly not in this case.

In additional tests, a rapid degradation of NHPI was observed in Alternating Polarity experiments due to this unexpectedly high current input. Such degradation leads to the unexpected product selectivity.

 

Accordingly, the group published their findings to highlight an equipment engineering concern that is likely to influence and inform optimization strategies for a wide range of synthetic organic electrochemical methods under development.

 

To ensure product quality and to further improve EletraSyn2.0, IKA has conducted a thorough inspection of the instrument as well as detailed investigation of this issue. It turned out that the varied cell potential was caused by the way ElectraSyn 2.0 controls voltage against the reference electrode.

 

Method of voltage control

 

In the default setting of ElectraSyn 2.0, potential difference between Working Electrode (WE) and Reference Electrode (RE) is controlled when Reference Electrode is ON. Such setting remains unchanged during the experiments. In the ElectraSyn 2.0 apparatus, the working electrode (WE) is installed to the left side of the reaction cell and the counter electrode (CE) is installed to the right side. 

However, WE and CE do not necessarily indicate anode and cathode in electrolysis. WE can be both anode and cathode. For example, if 1.2 V is applied, WE will play the role of anode and the voltage should be set as +1.2 V between WE and RE.

On the other hand, if -1.2 V is applied, WE will play the role of cathode.

Alternating polarity

 

During alternating polarity, what is expected is the cycle of applying +1.2 V between WE and RE, and then +1.2V between CE and RE.

However, in the current ElectraSyn 2.0 software, the voltage control remains between WE and RE during the entire period. This means that applying -1.2V between WE and RE may induce completely different reaction, resulting in the observed asymmetric current behavior. 

In other words, if ElectraSyn 2.0 could switch WE and CE during alternating polarity, the problem of asymmetric current will be solved. This function was installed in an updated software.

 

Software update

 

After our investigation in software development, the aforementioned voltage control method was implemented. Users are provided with the option of enabling/ disabling the alternate polarity, with the latest software version (0.0.026 / 0.0.027).

 

The new software version was validated by using following test. In the first test, the solution containing 0.114 M Bu₄NClO₄ with acetone/MeCN = 1/1 ratio was used. As pointed out by the Reid group, constant potential mode with reference electrode-ON and alternating polarity-ON gave asymmetric current (blue circle in Figure 15.). When the setting is changed as illustrated above, totally symmetric current was observed (orange circle).

This test was conducted with another solution, verifying symmetric current behavior in this case as well. 

Accordingly, we have concluded that, alongside the existing function, an updated software version (0.0.026 / 0.0.027) will enable ElectraSyn 2.0 to perform a constant voltage reaction with reference electrode under alternating polarity conditions.

 

We thank Dr. Marc Reid, his colleagues, and all our users for supporting ElectraSyn 2.0 and providing valuable feedback.