Secondments are invaluable training tools, especially for PhD students. In this blog post, I will highlight their importance.

In many PhD programs, and especially ITNs, ESRs have the chance to get trained through secondments which according to the definition are a „detachment of a person from their regular organization for a temporary assignment elsewhere”.  Secondments essentially represent a period spent abroad working in a different workplace (labs in our cases), focusing on a specific project. We could thus say that metaphorically speaking, they represent the equivalent of a mission for us for scientific growth improvement. But what do exactly secondments mean to us? And why can they be so important?

Like other forms of detachments, surely a contributing role is played by the push they provide in getting out of our comfort zones and routines, adapting to new environments and scientific approaches, and settings. However, they primarily represent a tool for broader expertise development and training. 

 These periods abroad allow us to work in different labs, focusing on specific projects that may be related to or detach from our primary research. The goal is to develop aspects of the project that we are either unable to explore in our usual settings, can only explore partially, or that may require the integration of different approaches. These experiences are thus invaluable for gaining new perspectives on research problems.

Additionally, these exchanges allow us to take advantage of local equipment and environments, providing flexibility and experience with similar software and tools, or even the opportunity to use new ones, which is also important.  Upon returning, we can merge and enhance the knowledge gained with our primary lab's expertise. In addition, they often allow us to dive into different research fields and learn or get a glimpse at the deeper and complex variegations of research allowing us to get a deeper understanding of the challenges to face. They may also allow us to address what we are facing in our field with a more informed perspective.

Personally, in fact, I have found these tools very insightful and useful. As a synthetic chemist, I often notice the tendency to think of molecules and chemical modifications in a somewhat more simplistic or "plain" manner, while the computational approaches explored in some of my secondments have allowed me to recognize the deeper complexity of the drug optimization and to understand that the process should never be reduced to a simple, two-dimensional view.

To sum up, my secondments have allowed me hands-on experience with computational software used in drug discovery, exposed me to different mindsets and approaches and even joined engaging scientific discussions which would have been less likely to happen! Secondments offer not only the chance to learn new techniques but also the opportunity to engage with diverse scientific mindsets and approaches. This opens up the possibility of meaningful collaborations that might not be possible or would happen differently if I had stayed in my home country.

These are just some of the many benefits: meeting other experts, hearing personal stories, and seeing how different paths and minds intersect, I do believe this fosters networking, and contributes to a shared European identity. The different approaches to the projects, meetings, interpretation of data and scientific papers, and software, even when using the same software or working on similar tasks, are intriguing and open-minding.

Therefore, I would define these scientific tools as essential allowing a better exchange, as they facilitate exchange. After all, isn’t scientific progress built on the exchange of ideas and discoveries (and thus minds)?

So that’s how I would spell/summarise them out as: 
Scientific
Enriching
Correspondences
On
Novel
Data-exploration
Matching
Engaging
Networking
Team-building
Strategies
 
Thank you, ALLODD and the European Commission, for supporting this!
Regards,
ESR7 Vincenzo Di Lorenzo

Summertime is usually the time of the year when things slow down, and the lab gets a bit quieter. A good time to catch up on reading all those scientific papers that accumulate throughout the year in my “to read” bookmark folder or as a pile of printouts on my desk. With the summer (at least in Berlin) coming to a close, this is a good occasion to reflect on practices of how to keep up with scientific literature – a topic haunting me at times given the almost infinite and ever-increasing number of interesting papers out there.

For me personally, scientific papers fall into two categories. Category 1 includes scientific papers that are directly related to my field. These are publications dealing with “my” target protein, or reporting synthesis procedures that I want to apply. The second category more broadly entails reviews, perspectives and case studies unrelated to my daily work. While I usually make time to read “category 1 papers” as soon as possible the latter ones accumulate in my web browser and on my desk.

Let’s first reflect on how to find relevant scientific papers. Probably the most obvious are field-specific scientific journals. Through a subscription to their article alerts, you’ll receive regular updates on new research published. A second strategy that I find useful is to use citation tracking for seminal papers, e.g. in Google Scholar. It allows you to discover the latest research building on these groundbreaking articles and thereby stay up to date on a research topic. Finally, I often find inspiration for readings in online discussion groups and blog posts. These channels have the advantage that they provide, apart from the references themselves, other researcher’s opinions, criticisms and ideas on the respective publications in the form of comments. Translated into the real world, journal clubs are a great opportunity to uncover new literature as well, and discuss it with peers of course.

Once the sources for relevant literature are established, we should turn to a more critical aspect: How to make time to browse and read scientific literature. One strategy to maintain a steady reading pace is to set aside dedicated time for reading. While this may work for some people, I never managed to uphold such a routine. Rather I try to use regular “downtime” for reading, e.g. during waiting time in the lab or commutes.

Finally, let’s review strategies for efficient reading and note-taking. During one of our early ALLODD workshops, I learned the following approach to scientific reading that I have since adopted: Starting from the abstract, I continue by reading the conclusions section of a paper. This helps me to decide whether the paper is worth a deeper read. If it is, I either focus on the figures and tables to identify paragraphs that hold the information that I am looking for, or I continue reading the entire piece from introduction to end. While reading, I like taking notes. I use colour-coding to highlight text and categorize my notes into “hypotheses”, “key findings”, “open questions”, etc. I also find it useful to summarize key points right next to a paper’s title. You may also want to highlight critical data, e.g. the potency of a reference compound that you may want to refer back to later. Likewise, some citation managers allow the addition of keywords or notes to imported publications, which can help retrieve studies at a later point in time. When your goal is comprehensive literature research on a given topic, you may want to compile your notes alongside screenshots and schemes into a larger document that summarizes the findings. 

In summary, keeping up with the literature next to daily lab work and writing a PhD thesis is a continuous and at times challenging task. Setting up article alerts, using citation tracking as well as leveraging social media helps to discover relevant publications. Whether you decide on a dedicated time for reading or squeeze it in during downtime in the lab, efficient reading and annotation strategies alongside citation programs help to manage the sometimes daunting amount of information.
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Do you have any strategies to find, read and annotate scientific literature? Feel free to share them in the comments section!

In October 2023, I had the wonderful opportunity to complete a two-month secondment at the CAMD (Computer Assisted Drug Design) lab in Urbino, Italy, under the supervision of Prof Giovanni Bottegoni. As a purely experimental biochemist, this was my first foray into an actual computational lab and I found the experience very enlightening. Of course, I had had previous introductions to computational methods and case studies from some of my Biochemistry courses, as well as from presentations at various conferences, and not the least from my fellow ESRs hailing from the computational side of the allostery field. However, in this case, I found the adage “experience is the best teacher” to be true. My hands-on use of tools such as Schrödinger and VMD showed me in a concrete way what it must be like to be a computational scientist, and I now have a better understanding of the typical workflow, as well as of the stakes of such work, including the balance between making faster versus more detailed simulations. Additionally, although my own training focused on proteins I was already familiar with from my experimental projects (the melanocortin receptors), several of my colleagues in Urbino were starting various new projects on completely different targets. This contrasts greatly with how experimental labs usually function with the focus remaining largely on related and/or functionally similar proteins across most projects. Despite this, at the CAMD lab, we could still help each other out, which fostered a real sense of camaraderie and a greater understanding of each other’s goals. I believe, now more than ever, that the future of science, and drug discovery in particular, truly relies on, not just one or the other, but the symbiosis of both computational and experimental methods. Thus, it is crucial to understand the possibilities as well as the limits of both, in order to lead to optimal collaborations.

Finally, I would like to highlight the backdrop of my journey into the computational world: the gorgeous city of Urbino, relatively unknown internationally, but a marvel of Renaissance arts and architecture, as anyone attending the recent ALLODD conference there surely noticed. I was happy to return once more and have the chance to say a quick hello to my former colleagues at the CAMD lab. 

More than two years have passed since I joined ALLODD and I am now delving into scientific conferences with one objective: share. Conferences are great opportunities to meet with people from your field and I was really amazed by the kindness of people who are always happy to discuss scientific ideas but also share their thoughts on career path. Among numerous insights, here are the most significant tips:

Be curious
As scientists, we enjoy uncovering new problems and devising innovative solutions. Cultivating a curious mindset involves continuous learning and staying connected with the latest advancements in your field and beyond. Embracing curiosity fuels your drive to seek out new challenges and opportunities with happiness.

Be focused
Establish clear career goals and remain resolute in your pursuit of them. A focused approach ensures that you stay on track and work diligently towards achieving your ambitions. By staying unwaveringly focused, you can navigate through the complexities of your scientific journey with purpose and determination.

Build a network
Whether your professional aspirations lead you towards academic pursuits or the industry, the value of building a strong network cannot be overstated. By fostering a network, you can create a supportive ecosystem that is vital for support, guidance, and opportunities. Funnily, I met at these conferences people who worked in Darmstadt, Germany (where I am currently living) or even in Clermont-Ferrand, France (where I studied). In France, we have a saying “Le monde est petit” (the world is small).
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Be unique
Last but not least. Each scientific journey is inherently distinct, shaped by individual experiences and perspectives. Embracing your unique attributes and experiences is a powerful way to differentiate yourself and pique the interest of others. By showcasing your uniqueness, you can carve out a compelling narrative that sets you apart in the scientific community 

​On 27th February- 1st March 2024 we ESRs had the great chance to get trained through the 3rd ALLODD Training School in the J&J campus in Beerse, Belgium “IPR Training for Researchers & ESR Presentations on the Progress of their Research”. 

It was a great opportunity to get in touch with the industrial world once again and experience also the personal stories of some of the speakers alongside training and information. It has been very interesting to get to know how the “big pharma” is trying to support innovation through several partnerships and founding even physical ones like the JLABS and get in line with the new guidelines like the project for the reduction of emission which Johnson will try to reach in 2026. Having a geothermal power plant within a campus is surely quite impressive!

Also, the attention to animal health care, it’s something I am sure people are expecting to see more and more applied and this is also a great achievement. Because if it is true that (unfortunately I would say!) they are still required, it is also true that our efforts can be applied even more in this sense, after all (trying to relieve pain isn’t what we should be trying to focus on?) I just hope we will see more and more of this in future and worldwide!

Alongside this, we had the opportunity to get in touch with very interesting talks like intellectual property and Project management and partnerships on the first day and scientific ones on Car-T cells therapy, PROTACs and the kinases. In sum a well-compelled series of talks ranging from biology to chemistry, medicinal chemistry and more! 

But this was not all, on the third day we had to practice (and I would dare to say re-learn!) how to introduce ourselves rapidly but exhaustively in a 4 and then in 1-minute pitches trying to catch as much as possible, which is surely not an easy task! Yet it is interesting to get a little detached from our daily way of expressing ourselves within the scientific community and get more to the general public. After all, as George Orwell has greatly shown in 1984 behind simplification there can be a huge work, but I would add sometimes this can also be very beneficial! 

All this simplification process is in fact one of the basic sets for effective communication in which a key role is also relying on intonations, gestures, and looks and is always very important to keep in mind!
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We cannot be thankful enough to ALLODD and Janssen Pharmaceutical for this experience and further opportunity and as learned from hearing the story of Janssen himself, proceed even with more enthusiasm cause the clock is ticking and “patients are waiting”. And after all, we are scientists, and we hope to give our contribution also to help! 

Lessons in Chemistry is a miniseries that tells the life story of chemist Elizabeth Zott in the 1960s. Unfortunately, she is not a real person, and chemistry only serves as a secondary character, blending with the atrezzo. However, I’m still going to take advantage of this blogpost to quickly talk about my real passion: TV shows.

In this case, this show is based on a fictional book of the same name, so the leading scientist didn’t exist. Nevertheless, the situations she goes through and the life she ends up living can easily be assumed to be an accurate representation of those times. Telling the story of a female scientist in 1960s US, it obviously deals with misogyny and the role it played in hindering and even truncating many women’s careers, still reverberating to this day. And to this viewer-reviewer, the interesting part is that these topics are depicted in a markedly refreshing way. Although none of it is novel, instead of softening, dumbing down, or sugarcoating situations of rampant sexism, for example, I found that the scenes are laid out with such rawness that they felt truly authentic. In an age of mass-produced entertainment extruded by Netflix and the algorithmic feeling of everything it puts out, in Lessons in Chemistry I could appreciate a specific and differential creative vision and drive; a human heart behind it, in short. I personally like to imagine that such a human is Brie Larson herself, who serves as the lead actress and as a producer, and whom I found to have delivered an amazing performance, supported by a very effective cast.
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Sprinkled on top, we get some corny lines supposedly pronounced during the inception of nucleic acid research, and others about the chemical reactions that take place when food is being cooked. Both are blurted out by the actors as meaningless strings of words that they were told to memorize, but I didn’t pay attention to their scientific rigour and also it doesn’t matter. Chemistry here is a background character used to arrive to the conclusion that we can’t control for every variable, but uncertainty may lead us to places we’re happy in. Ew. Also as a background element used to move the story forward, our heroine gets entangled (ew) with a man who is a fellow scientist. But this character diligently reinforces the accuracy of the “men written by women” online phenomena, as there’s no way this person ever existed or even could exists nowadays, but that may be a topic for another blogpost. Overall, Lessons in Chemistry amounts to a non-scientific well-made and enjoyable show, and its complete first and only season just wrapped up and is available on Apple TV+.

In the fast-paced world we live in, one secret to success is to manage time efficiently.  During our ALLODD meeting in Budapest [1], we had training on how to increase productivity through efficient time management.
In this blog post, I would like to share 7 key points:
1.     The Three Pillars – environment, mind, schedule: Organise your working space to minimize distraction, clear your mind from thoughts by taking notes, and structure your day using the 18-minute/day method.
The 18 minutes consist of 5 minutes dedicated to planning the day, 8 minutes to refocus every working hour, and 5 minutes at the end of the day for reflection.
 
2.     Estimate time: To estimate work durations, use historical data or tools like the GANTT chart (Figure 1 A) to analyse the critical path and to spot bottlenecks that require the most time.
 
3.     Feedback: Find the correct timing to ask for feedback to ensure that the work is following the correct focus required for completion.
 
4.     Prioritization: A distinction between important and urgent jobs helps in setting priorities (Figure 1 B). Important and urgent tasks such as responding to accidents, giving a short minute presentation for important collaboration opportunities, or responding to a review are called firefighting tasks. These tasks are generally managed well.
More challenging is to balance reactive and proactive tasks. Reactive tasks such as responding to e-mails or spending time on social media are loud, meaning we are notified regularly, while long-term proactive tasks such as career development or working on a paper/project are quieter.  It is important that moderately urgent tasks do not get overshadowed by urgent ones.
 
5.     The Power of Habit: Understand that habits play a significant role in time management. Cultivate good habits that align with your goals as this can help to master periods of large change such as moving to another country or working for some time at another organization/university.
 
6.     Small Changes: Don't underestimate the impact of small changes in your routine. Consistency is key.
 
7.     Elephant vs. Rider: Imagine your conscious mind as the rider on top of the elephant (habit) (Figure 1 C). It needs time and conscious efforts to guide your habits toward effective time management.
Many of the points were known to me before the training, but the refresher reminded me to incorporate these techniques into my daily routine. I started to integrate the refocusing every hour to help me improve my productivity in the last two weeks. 
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[1] Time management, Trainer: János Balázs KISS, Mindbeat, September 2023 

I've reached the exact midpoint of my fellowship, and it has been an incredibly transformative 18 months! From relocating to three new countries, connecting with ALLODD members, and going deeper into my project, it has been a whirlwind of growth and exploration. The experiences I've encountered during this time have undoubtedly broadened my horizons, and there's still so much ahead to embrace!

Two topics that have particularly caught my attention recently are machine learning and AI in science. During my two-month secondment in Athens and the insightful conversations with my peer there (thanks again for our discussions 😊), I've become a bit less naive about the topic. While I've used chatGPT for travel tips before, I now recognize that machine learning and AI have a profound impact on the future of science.

As more and more pharmaceutical companies are venturing into AI and machine learning to transform their processes, embracing these new technologies is crucial also for bench scientists like me. While the predictions I've received might not always be accurate, the real power lies in the way these tools streamline and narrow down possibilities. In the fast-paced world of science, time is a precious asset, and AI serves as a valuable ally, empowering scientists like me to make more informed decisions, faster.

Looking ahead to the next steps of my PhD journey, I'm filled with excitement and curiosity. The best is yet to come!

Chemical space is vast. So vast, that screening even a relatively small portion of this space within a drug discovery campaign is close to impossible. Just considering molecules with 30 heavy atoms consisting of carbon, oxygen, nitrogen, and sulfur we would find more than 1060 possible combinations [1] - a number that make even industry-scale million-member libraries of compounds appear small. While these libraries are still successfully used in high-throughput screens, a different approach, coined fragment-based drug discovery (FBDD) over 20 years ago [2], makes use of collections of so-called fragments with lower molecular weight (<300 Da) and a limited number of structural features [3]. The small size of the fragments drastically decreases the number of possible molecules and enables FBDD approaches to cover broader chemical space more efficiently. Due to their low complexity and low number of ‘non-essential’ atoms, screening fragments usually yields higher hit rates of molecules whose interactions with the target are defined by only one or two high quality contacts and high ligand efficiency (binding free energy per heavy atom). Accordingly, FBDD routines can be instrumental in finding druggable ‘hot spots’ and defining starting points for lead discovery. Yet, with small size often comes low affinity. Probing weak protein-fragment interactions demands for highly sensitive biophysical techniques, such as NMR, X-ray crystallography, surface plasmon resonance (SPR) or thermal shift assay (TSA), which often depend on availability of the purified target and yield only limited information on the effect the targeted site has on the functionality of the protein in a physiological environment [3]. The latter is particularly important for allosteric proteins considering the diverse mode of actions allosteric modulators can exert. Functional cell-based assays would allow for such a read-out in the absence of soluble target protein but are limited by the high concentrations of the fragments necessary to induce a measurable effect.
 
One way to mitigate the challenges of detecting low affinity fragments, is so-called covalent tethering. In equipping fragments with a warhead that can form a covalent bond close to the target’s binding site, tethering increases the effective local concentration and therefore also apparent affinity. Reversible disulfide-bond formation between a thiol-modified fragment and a free naturally occurring or genetically inserted cysteine on the target is probably the most frequently used method to trap interacting fragments at the target site [4]. Most prominent example for this approach is the discovery of a covalent allosteric inhibitor for K-Ras G12C [5]. Recently, this approach has also enabled validation of the mode of action of a low-affinity allosteric fragment for PTP1B [6].  However, cysteines often represent critical sites for disulfide bond formation, posttranslational modifications and can be highly abundant throughout the target and off-target structures. Accordingly, disulfide-based tethering can often not be applied in cell-based assays and requires careful optimization and validation. In particular, if the cysteine is introduced by mutagenesis.
 
In a recent paper, Mattheisen et al. [7] present an alternative elegant approach that leverages bioorthorgonal coupling chemistry to tether ligands to the class A GPCR C-C chemokine receptor 5 (CCR5) for functional fragment screening in live cells. Due to its critical role in HIV-1 pathogenesis, CCR5 has been rigorously characterized in terms of structure, function and druggability. Likewise, allosteric antagonists and the corresponding allosteric binding site have already been identified making it an ideal system to establish the proposed method [8]. While no large-scale fragment screening is conducted, the study provides a proof-of-concept and explores important considerations when establishing such a system.

The system consists of a chemical handle that is incorporated into the receptor close to the allosteric binding site (Figure 1A) that can react with a reactive functional group under bioorthorgonal conditions compatible with mammalian cell culture (as introduced by the Bertozzi lab [9]). The reactive warhead is linked to a ligand via a PEG spacer, allowing a potential, now covalently coupled, antagonist to reach into the allosteric pocket which lays deeply buried in between the receptor’s transmembrane helices (Figure 1B). Functional response upon reaction with this heterobifunctional ligand is then probed by assessing cellular response to an agonist (Figure 1C). Using a combination of molecular dynamics simulations and subsequent experimental validation, Mattheisen et al. optimize assay conditions and controls by varying insertion points of the chemical handle in the receptor, warhead chemistry and linker length. Throughout the optimization process, the FDA-approved CCR5 antagonist maraviroc (mvc) is used as an active antagonist on the heterobifunctional ligand, which worked nicely for showing the theoretical potency increase the covalent tethering yields. So far so good. But mvc is a highly potent antagonist with nanomolar activity after all. So how would this system perform for lower affinity compounds, such as fragments?
 
To test the capability of the system to distinguish between non-binders and low-affinity binders, six heterobifunctional ligands carrying low affinity mvc analogues were synthesized and tested in two cell-based assays, one testing for ability to block agonist activity and the other for blocking labeling of the reactive handle by a warhead-fluorophore conjugate. Intriguingly, this strategy revealed that only those heterobifunctional ligands whose low affinity mvc analogues show antagonist activity would also block labeling of the reactive handle by the fluorophore. Moreover, only the receptor containing the reactive label was inhibited. This is an important observation, since it indicated that on the one hand, the potency of low affinity compounds is effectively increased by covalent tethering and that on the other hand, affinity of the fragment for the pocket is the driving force for the reaction.
 
In summary, the paper presents an innovative approach for live-cell functional screening of low-affinity compounds that adds another valuable method to the drug discovery toolbox for pharmaceutically interesting GPCR targets. However, some open questions remain: How easily is this system transferable to other receptor classes? How does the system perform in large-scale fragment screenings as shown for disulfide-tethering? How does it perform in a direct comparison with biophysical fragment screening in terms of hit-rates and false-positive rates? Can it facilitate fragment-to-lead discovery?

References
 
1. Bohacek, R. S., McMartin, C. & Guida, W. C. The art and practice of structure‐based drug design: A molecular modeling perspective. Med. Res. Rev. 16, 3–50 (1996).
2. Shuker, S. B., Hajduk, P. J., Meadows, R. P. & Fesik, S. W. Discovering High-Affinity Ligands for Proteins: SAR by NMR. Science 274, 1531–1534 (1996).
3. Erlanson, D. A., Fesik, S. W., Hubbard, R. E., Jahnke, W. & Jhoti, H. Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discov 15, 605–619 (2016).
4. Erlanson, D. A., Wells, J. A. & Braisted, A. C. TETHERING: Fragment-Based Drug Discovery. Annu Rev Bioph Biom 33, 199–223 (2004).
5. Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A. & Shokat, K. M. K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503, 548–551 (2013).
6. Keedy, D. A. et al. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Elife 7, e36307 (2018).
7. Mattheisen, J. M. et al. Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells. J Am Chem Soc (2023) doi:10.1021/jacs.3c00972.
8. Tan, Q. et al. Structure of the CCR5 Chemokine Receptor–HIV Entry Inhibitor Maraviroc Complex. Science 341, 1387–1390 (2013).
9. Prescher, J. A., Dube, D. H. & Bertozzi, C. R. Chemical remodelling of cell surfaces in living animals. Nature 430, 873–877 (2004).

Just last week, I attended my very first conference: an ALLODD one, no less! Held in the understatedly beautiful city of Strasbourg, this event was my first chance to finally meet my fellow PhD students in-person, after joining the program 5 months ago. Thankfully, three of them had already visited me in Athens, which made the initial apprehension of facing a group of 15 new (but amazing) people much easier.

The first two days of talks proved intense and demanded all the brainpower we could muster. But once the talks were over, we still had the perfect opportunity to replenish it, just as ‪Ilpo Vattulainen‬ advised, by eating Alsacian-style fish during the planned social events. Nonetheless, it was interesting to hear firsthand about the current role of allostery in research, both from the academic and pharmaceutical perspectives, after having spent countless hours reading about it in my first months of PhD.

On the third day, I was finally able to hear my colleagues explain their projects and share their progress in their own words. It is always alluring to learn about science outside one's own tiny research niche, and to witness the seamless flow of discussions that arose between different fields of research.

Attending the ESR-exclusive training activities (and equally importantly, our own unplanned socialization events after) was an invaluable opportunity to share and discuss between us about the challenges and achievements of undertaking a PhD, and find support in one another. I appreciated the chance to get to know my peers on a more personal level, exchanging stories and experiences, and realizing how serendipity brought us all together from different places and backgrounds.

As my TGV departed from Strasbourg, I was left with a pleasant sense of fulfillment and growth. And an even more intense urge to meet everyone again in just 4 months! See you soon.