Flow ideas: Expanding the possibilities in Med Chem

Just read an article (Molecules 2014) on flow through hydrogenations through the eyes of a medicinal chemist….sort of. A combination out of Baxendale and Ley is a contribution in the area of heterocyclic construction using an appropriately placed hydrogenation of an aromatic nitro group, strategically located to take place in a subsequent reaction to form advanced riboflavins, quinoxalinones and benzodiazepines…..each important in their place as strong pharmacophores.

Two things that stick out to me as important: how do they arrive at a final working method and what were the issues….when you read an article by these authors it will inevitably have this information present and that is the type of discussion that will help push the area of flow chemistry forward. For instance, in the first scheme below, the group needs a diamine functionality and over-reduction of an aromatic halogen took place with Pd/C but not with PtO2 (ha, how many times have you read a BIOMCL — the things that don’t work are not discussed)— and this is likely made more challenging by the fact that they had to heat the reaction to 45C for the reaction to work well and use MeOH to keep the materials in solution for the duration of the reaction. The nice thing about the reaction is that it was easily be performed and optimized for catalyst using the H-Cube by ThalesNano. Another piece of anecdotal information — the diamine is typically not stable for any appreciable length of time — but can be used in the subsequent step. The scheme below indicates the two possibilities for the reaction — and note that the condensation here was done in batch fashion for 10 hrs at room (must decompose the diamine with heat because 10 hours is a long time).

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Although they applied the same methodology to a quinoxalinone series, I am going turn our attention to the work done on benzodiazepines. Work on the scaffold is traditionally considered older — with new developments as a rarity — I know my early research included an aza-version of this and it felt like a total synthesis. For the storyline, some conditions needed some attention in order to move to a complete flow system. For example to build the amino-nitro diarene, they chose a microwave mediated SNAR reaction of a fluoro-nitro arene and the requisite aniline. Fortunately, I have discussed this type of reaction in a past post so there is some development utilizing this approach — in this case, however, the aniline is deprotonated with LHDMS and irradiated in the presence of the fluoroarene to produce the diaryl scaffold in high yields in a short amount of time. The product was redissolved and hydrogenated and cyclo-dehydrated to provide the benzodiazepine in high yield. To adequately handle the dehydration, an in-line MgSO4 filled glass Omnifit column was placed subsequent to the flow hydrogenation (again – H-Cube with in-line MgSO4).

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The great thing about the microwave method is that it provided a good reaction starting point for a medicinal chemist planning a library for some initial screening hits. The bad news is that scale-up in this fashion would require a different microwave or a continuous flow method if additional testing or to get the compound through an entire cascade an on its’ way to animal studies….this group recognizes this as a key criteria in developing the technology and therefore worked out a method for the first step in a continuous format. Prior to jumping into the flow conditions, the 2-step process provided a nice route into the desired compounds with microwave (1) and flow (2) method.

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In moving over to the flow conditions, the base and mixing were critical for the execution. Although the scheme helps you follow the format, three separate lines were used to form a good process with n-BuLi in channel A, the amino-benzophenone in channel B and the fluoroarene waiting in channel C, with the appropriate mixing chambers and T or Y-lines adjusted to provide the mixing and timestamps for delivery of reactants/reagents. The initial solutions for deprotonation were cooled to 0C, mixed for a quick reaction and flowed into a flow stream of the electrophile. Once this last mixing is started, the flow went into a heated coil loop (52 ml) at 115C for the cyclization to proceed. Once the product was formed, the group added a process to quench and work-up the reaction so that the desired solution of organic product (plus the addition of MeOH if needed) would flow into the H-Cube midi under similar conditions indicated above (5 bar, 45C, 2.2 ml/min, coil loop, PtO2) provide up to 120 mmol or 38.1 g. The in-line work-up process is certainly worth a detailed read — this is an area of discussion that chemists will eventually develop innovative ways of handling reactions that include lithiations mid-stream (and other transformations)…although we would like to make everything plug-and-play, we need to make sure to understand what’s in the line to have a successful flow method in the lab. Happy Reading!

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Flow – in review: you are part of a movement

Let me start off by saying that I haven’t had the opportunity to meet Ian Baxendale, but in taking a look at his group at Durham University and reading one of his review articles on enabling technologies (The Integration of Flow Reactors into Synthetic Chemistry: J Chem Technol Biotechnol 2013), I would have to say that I hope to in the future, unless of course he is a Man U fan.

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Information and technology have certainly changed the landscape of synthetic chemistry the way we know it today. I still remember using chem draw for the first time, lol! And now, microwave and flow technologies are the real ‘game changers’ with the days of being stuck in a round bottom flask can be thought of as fondly as the bunsen burner — it’s been over 150 years – what would Woodward do now?

The way it used to be, maybe old-school……

The general thinking in organic chemistry was to be as good with the mechanism, selectivity, reactivity and disconnection to remove the side-reactions and have a reactive intermediate survive to the product – but it was always counter to what I was used to hearing – heat it up some more – well that doesn’t add up, because reactivity and stability don’t often correlate – the hammer and tongs should be placed in the drawer – microwaves often satisfied, since a high percentage of reactions do benefit from heat and are robust enough to react quickly (and to be honest the inorganic community would second that notion and they get a tremendous boost). But we should strive on the organic side to gain something from emerging technologies which help us look deeper into the chemistry. The is often counter to many medicinal chemistry departments looking for a 1000 compounds out of each chemist – so they turn into good fisherman and poor synthetic chemists – what I mean is that a reaction can be poor but they can use improved HPLC techniques to obtain enough compound to test – yikes…..my experience is that this slows drug discovery because the cost of resynthesis is high compared to making enough compound to get through the testing cascade in the first place.

Ian helps us restep our tracks a bit and think about mixing and reactivity, but more importantly how to think about developing more efficient and optimized synthetic strategies. He mentions what we know — purification and backend characterization have been strong for many years and there is no reason why we should improve the frontend. That should make us feel a bit better at night after a long day in the lab.

At the risk of speaking for Ian, we need to be a bit more mindful in a positive way to the integration or marriage of chemical engineering and synthetic chemistry – and this has been done over the last 10 years in a fruitful way. Both disciplines have been doing their thing for a while now, with flow processes in place for over 20 years, but each in separate silo without a need to find the other.

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Ian takes us out of our comfort zone and talks about the conceptual approach where reactions can be run in tandem through several reactors without the need for solvent switching – [cartoon of round bottom to round bottom to flow ]– he then brings us back and mentions that this is not an ideal world and we would be faced with quenches, and solvent changes and such due to the nature of reactivity in synthetic transformations. However, we can get close by combining the technology with solid-supported reagents and scavengers (and liquid separators) to maintain a continuous flowing sequence.

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Solid-supported reagents and scavengers in flow chemistry

Solid supported reagents have been used extensively in multi- step organic syntheses in batch. Ideally, the use of such reagents should provide clean products without chromatography, crystallization, distillation or any traditional work-up procedures. Supported reagents are reactive species that are associated with a heterogeneous support material. They transform a solution resident substrate (or substrates) into a new chemical product (or products), with the excess or spent reagent remaining tethered to the solid matrix making separation a simple process. In a similar fashion, impurities can be removed from a flow stream using a scavenger species immobilized on a support. This scavenger creates either an electrostatic or covalent interact with the impurity, sequestering it from solution and binding it to the solid matrix thereby effecting purification of the reaction stream. By utilizing these supported components packed into simple columns or reactor cartridges it is immediately possible to perform multi-step organic sequences employing an orchestrated suite of supported reagents to effect all the chemical transformations and purifications.

An illustration of this concept is shown in the formation of 4,5-disubstituted oxazoles from an isocyanide and an acid chloride, facilitated by cyclizing the reactive imidoyl chloride with an immobilized PS-BEMP base. Any excess acid chloride was then trapped with a benzyl amine resin in-line column to provide the desired compounds in >95% purity in high yields. Comparing a traditional batch method where yields are greatly diminished. Running the system for ~12 hr provided 10-25 g of material if needed – showing that scaling-out will be an straightforward process.

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Reactive intermediate flow methods need to have a solid foundation for chemists to use the technology and it is a must to be able to trap undesired materials in order for the reactive intermediate to flow through the sequence – an example used here utilizes a Curtius rearrangement with an acid or acid chloride to form the reactive acylazide which undergoes rearrangement to form the isocyanate and reacted with nucleophiles to form the desired product – alternatively, DPPA can be an effective alternative in large scale flow reactions where excess acid is used and the resultant coil performs the rearrangement with an immediate quench with the nucleophile on the backend of the flow sequence. In-line acid-base scavenger columns and an acyl-azide Merrifield resins have been utilized to facilitate the reactive intermediates moving forward and the undesired materials trapped from further participation.

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DPPA modified Curtius rearrangement

OK – the review is exciting, but I don’t want to rewrite it. I will leave you with the thought that technologies can be combined in cleaver ways as added to value to each. Several examples of microwave flow examples can be done simply by building a coiled reactor that can be placed in a multi-mode microwave – there are two examples shown below, one with a glass coil with modified caps and the second with a Teflon reactor case with fluoropolymer tubing that can be exchanged in volume, diameter and length.

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Additional microwave cavity inserts – tubing can be modified on need

Ian goes on to additional configurations and multi-stage/step approaches with these concepts in mind including several different types of reactors with the ability to trap or react the way the chemistry needs. He then goes into great detail on the diagnostic end and the data handling and how we can scope and optimize the chemistry, and finally ends with several examples of the application of the technology in drug discovery – from library generation to optimizing a lead compound. I hope you enjoy the review as much as I did and it generates some thoughts and discussion within your research groups. Happy Reading!

Microwave to Continuous Flow Tech Transfer

I’m not sure if it was in the generic scheme of the reactions performed, the authors of the work or the title translating microwave methods to flow that got me: truth is it was a bit of all three in a recent publication (Beilstein JOC 2011). The scheme had a para-nitro diaryl ether, which for me means an amine handle with multiple substitution patterns on both rings — reliving my sorafenib days at Bayer ( I did a lot of Ullmann reactions, uugh, although the microwave did prove handy!). The authors of course are front and center of the flow chemistry community and lastly there have been a number of papers taking microwave methods and transferring them into flow methods — and I do believe we will see more of these. It’s meaningful and there are advantages to both.

Although Dr. Watts and Dr. Wiles probably didn’t have kinase inhibitors in mind, the para-amino diaryl, heteroaryl motif and diaryl motif is found bountiful in the literature. So taking an illustration of a microwave model from JD Moseley (Org. Biomol. Chem., 2010) and later work by O. Kappe and JD Moseley (Green Chem 2011), they studied and compared micro-reactor and microwave approaches to the reaction scheme below:

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For a starting point, W/W point to the studies by M/K’s stop flow microwave conditions and point to the lack of energy benefit in using microwave conditions on a larger scale due to the limited penetration depth and lack of energy efficiency. Add to this in both a batch and stop-flow capacity where the heating and cooling in a microwave mode does not help the cause. All true, although I would point out that with auto-sampler and improved cooling in many of the latest microwave developments (Anton Paar, CEM), the man hours to make libraries of compounds would be the more efficient technology.

To perform the flow experiments, W/W used a Labtrix S1 (Chemtrix) (shown below). The system consists of a glass micro-reactor that is positioned on a thermally regulated stage, which enables reactions to be performed between −15 and 195 °C. Reagent solutions are delivered to the reactor through a series of syringe pumps (0.1 to 25 µL·min−1) and the system is maintained under a back pressure of 25 bar, which enables reactants and solvents to be heated above their atmospheric boiling point whilst staying in the liquid phase. The reactant flow rates, reactor temperature and sample collection point is automated and the system has an in-line pressure sensor that monitors the system pressure throughout the course of an investigation. The software enables the effect of reaction time, temperature and reactant stoichiometry to be investigated in an automated manner whilst the system is operated, unattended, within a fumehood — the software is something where the flow manufacturers have developed a much more extensive data retrieval and display compared to their microwave counterparts – although I do like the onboard screens on the microwave for daily operation.

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Using a two-feed system they are able to control the reactants, temperature, flow-rate and stoichiometry of the reagents and base during the studies with a reaction time of 10 minutes to compare to the microwave method. The first set of results were nearly identical to that of the mw method. While it is a side note, it is fair to mention that one of the positives of flow is that nearly all solvents can be used for experimentation and for microwaves, one has to choose how to handle the situation. Not all solvents absorb microwave energy….and with that, a choice of absorbing material or vessel will need to be made for the reaction conditions. The nice thing if you look at the conditions used, 195C with a max of 25 bar of pressure will allow most organic solvents as an option under these conditions (hexane, CH2Cl2, toluene, EtOH, EtOAc, Dioxane, MeCN, DMA) in a microwave set-up.

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Following the initial set of experiments, they found a reduction in reaction time for this reaction from 10 minutes to that of about 1 min to complete the reaction. In addition, MeCN was a suitable replacement for DMA — which will work for either technology. In addition, with the feedlines separating organic base for the other reactants, they screened a number of bases to identify the best choice with some striking differences in bases used. Although we can all probably decide in retrospect which bases would have or did provide the best results, the ability to screen and scope reactions provides an excellent way to move from small to large scale methods in a data driven format.

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Now that I talked about some of the basic features in the paper, I will leave the rest for you to dive into — there are additional efforts made to understand the reaction with several different substitution patterns, a move from organic bases to inorganic bases — a nice added value with biphasic aqueous inorganic bases used, where mixing can be employed in microfluid development of reaction conditions. This was a nice example of a transfer of technology from microwave to micro-reactor conditions with pluses in a number of areas — and some things to think about where microwave conditions can be used as the preferred method on small scale. Overall I think these are the things that should be discussed at length as a strategy is being developed for a particular project — both showing the capability as an enabling technology depending on the application need. Happy Reading!

Modern Research Chemistry: MW and continuous flow Indole synthesis

In a continuation in theme of my interest in indole synthesis, I found a fantastic mini-review on-line by Nadeesha Ranasinghe and Graham B. Jones at Northeastern University Dept. of Chemistry (Current Green Chemistry, available as an e-article and inprint 2015) on Flow and Microwave Assisted Synthesis of Medicinally Relevant Indoles…..this will be a must have for anyone interested in flow, microwave, or combination of the two as enabling technologies. And on a side note, Graham is a Liverpool football fan so that has to count for something.

Let me digress just a bit, because there have been so many advancements in the last 5 years, that one has to take a step back and see how it fits as we move away from traditional approaches to newer, current sustainable processes. We are at a pivotal point in our field* For a number of years our mechanistic understanding has been beyond our abilities to execute them, but now we are seeing the creativity amongst chemists at an accelerated rate with enabling technologies in microwave and flow chemistry methods. For the first time – we are reaching for the newest tools in the box to develop strategies that support our ideas and mechanistic creativity. Part of this growth is in line with automated purification and detection, as well as major advancements in X-ray and modeling technology – we are equipped to elegantly move forward over the hammer and tong approaches in the past.

Now that I got that out of the way, let’s go through the review – I will focus on flow and you can read some of the indole microwave details along with several installments on mw assisted indole syntheses at http://totallymicrowave.wordpress.com/, but the last section on the combination of the two will be covered briefly. The review does take a start with an historical perspective on the significance of indoles and their place in medicinal chemistry and drug discovery and changes gears to say that there has been focus on changing the way we perform our chemistry with newer strategies on-line. Jones describes two important points here: 1)that within enabling technologies is “enabling techniques” and that this is any technique that speeds up a synthetic transformation, facilitates easy work-up ad makes isolation/purification simple — all areas in alignment today….the only thing I would add is that it is sustainable; 2) changing the mindset of scale-up to “scale-out” as an underlining mantra to flow chemistry (i.e. we don’t have to change the chemical methodology from a traditional batch method if we start with a flow method, so we are simply using the chemistry in a larger capacity. OK, enough of that.

Early indole flow: the first pioneering effort to indole flow chemistry can be attributed to Paul Watts (Tetrahedron 2010) where he compared 3 methods to a conventional batch method.

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A second milestone came from the work done by O’Shea and Tricotet (Chem Eur Journal 2010) where they generated a series of 3-hydroxymethylindoles in an automated set-up with 2 flow steps and an in-line extraction module to trap and send the components through the remainder of the set-up, indicating that it is possible to perform multi-step flow chemistry in a straightforward way.

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Moving into some of the more mainstream instrumentation available, Guillier reported a continuous flow hydrogenation in the formation of indole and 5-azaindole-2-carboxylates, a Reissert Indole construction, using an H-cube (ThalesNano) with pre-packed heterogenous catalyst cartridges with a flow of 1-3 ml//min and a temperature range of 20-100C ( J Flow Chem 2011).

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A example of approaches can also be found in approaches to defined important indole intermediates. For examples, Kappe reported a flow route to 7-ethyltroptophol without the use of strong acids and bases — indicating we can move away from harsh conditions utilizing a flow approach (Org Process Res Dev 2013).

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As I mentioned prior, I will highlight additional microwave approaches elsewhere, but it does serve to mention a couple of examples of the combination of mw and flow, or even areas where the transfer of technology is applicable in moving from mw to flow chemistry. For the first report on the combination of the two for indoles (MACOS) featured a simple flow cell made out of glass fitted with sand, attached to an HPLC pump for solvent flow and a back pressure regulator to produce 1g of the desired indole in 15-30 min @ 150C (91% isolated yield) (JOC 2005)……interesting that this combination pre-dates full use of flow methods.

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The transfer of technology that is taking place can be found from microwave methods being used as a baseline for conditions to be used in continuous flow set-ups. Kappe published an approach to mimic microwave conditions in comparison using a stainless steel microreactor (spec, 350C and 200 bar capability) to produce 25 g of an advanced indole in 1 hour (EurJOC 2009).

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The last example of an advancement of the combination is reported by Michael Organ (Chem Eur Journal 2008) where he illustrates the use of Metal-coated capillary tubes traversing the microwave cavity under flow control for sequential aryl amination/heck reactions in the construction of substituted indoles.

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So hopefully this has helped with some perspective on the evolving field of continuous flow and combined approaches today. I thank Nadeesha and Graham for putting together a fabulous review for those of us interested in flow and indole chemistry. Happy Reading!