As A Computational Chemist in the Pharma Sector

As A Computational Chemist in the Pharma Sector

Author: Gian Asara, Melchor Sanchez-MartinezORCID iD

Dr. Melchor Sanchez-Martinez is a Senior Research Scientist in computational chemistry and data science working on drug discovery and development at Molomics, Barcelona, Spain. He talks to Dr. Gian Asara for ChemistryViews about the fascination and challenges of his job and what makes it so exciting.


Tell us a bit about how your career has developed, please.

After graduating in biotechnology with a Bachelor’s degree, I decided to pursue an M.Sc. in biophysics. During that year, I was introduced to theoretical chemistry, which I realized was my passion. So I decided to pursue another M.Sc. in theoretical and computational chemistry. During that year, I met Dr. Ramon Crehuet, who become my Ph.D. advisor for the next four years at the Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), in Barcelona, Spain.

When I finished the Ph.D., I had a formal postdoc offer from a research group in France, but for personal reasons, I decided to remain in Barcelona. At that point, it was clear to me that I wanted to do something at the borderline between computational chemistry and, if possible, pharmaceutical research, where computer-aided drug design is now a commonly used technique in the discovery and development of new drugs.

Before my Ph.D. defense, I started to work at Mind The Byte (MtB), also in Barcelona, a startup devoted to developing new computational chemistry software for the pharma- and biotech industries. We provided consultancy services, acting as a Clinical Research Organisation (CRO) in computational chemistry and related fields such as bioinformatics. A CRO company supports the pharmaceutical, biotechnological, and/or medical technology industry in the form of research services that are outsourced on a contract basis.

MtB regularly participated in regional, national, and Europe-wide funded projects. I joined the company as a computational chemist and progressed to Scientific Director. In addition to drug discovery, MtB gave me experience in real-world business operations, such as the acquisition of our main national competitor.

I experienced the growth of the company from being four and a half people—the project manager was working half-time—to almost 30 employees; there, I had the opportunity to supervise B.Sc., M.Sc., and even a Ph.D. thesis, and I was the principal investigator in most of the funded projects. I felt like it was a part-time academic job, because I did the research I wanted and published it, and a part-time industry job, because I had to fulfill obligations regarding team management, attend meetings with customers, and participate in consultancy projects.

I left Mind The Byte after four years to join Molomics in March 2019 as a Senior Research Scientist in computational chemistry and data science. Molomics is a company that advances the search for structurally new small molecule therapeutics using artificial intelligence (AI) empowered by human knowledge. It is a new approach and although Molomics is still a young and small company, it has great potential. In Molomics, I look for candidate molecules to became therapeutic agents against central nervous system (CNS) disorders, mainly Parkinson’s disease.

Since 2015, I have also worked as a course instructor at the Universitat Oberta de Catalunya, a private university based in Barcelona, in the M.Sc. program in Bioinformatics and Biostatistics.


What do you do in your current position at Molomics?

I am a scientist. I do research and, eventually, I also publish it. I am responsible for carrying out and managing drug discovery projects to increase and advance Molomics’ drugs pipeline. I lead some projects and collaborate on others, mainly in structure-based drug-design activities.

At Molomics, we try to develop our molecules as far as possible in the drug-discovery pipeline. Instead of just taking care of a single or a few steps of the drug discovery process (i.e., predicting a list of molecules that are active against a protein, and never getting to know if any of them become a hit or a lead) we try to be an active part in as many steps of the discovery process as possible. We check the validity of our predictions by ourselves, which is really rewarding. Also, such an approach allows us to improve our predictive models and computational chemistry tools. As we are a purely computational company, the experimental testing is done by our collaborators, as well as by CROs. I am responsible for coordinating both the computational and experimental parts of the discovery process for the projects I lead.

This is a challenging part of the job: You need to be an effective communicator and be able to work with people from different fields. Communication is vital. Also, a deep understanding of what you do but also from what other people do is needed. The learning curve is always steep!


How much is your job related to chemistry?

100 % related. I work with molecules all day. Biology (biotechnology- and biochemistry-related concepts), computational chemistry, and chemoinformatics are my day-to-day tools. Computer science, i.e., programming and data science, is also a very important part of my daily work—but always in relation to chemistry.


What other skills do you need?

In addition to a solid chemical background, you need to have a deep understanding of some biological and pharmacological concepts. Programming and data science skills are vital. System administration skills are also welcome but less crucial.
Soft skills are also important, such as being open-minded, eager to learn, and able to work both independently and as part of a team.


Please tell us something about your daily routine.

My main work is to carry on my research. I use computational chemistry and cheminformatics tools to discover new small molecules that are good candidates against certain diseases. I study the proteins involved and analyze drug-target binding and interactions. I also regularly develop new software tools, workflows, and QSAR (quantitative structure-activity relationship) or machine learning-based models to add a new element to our toolbox or to improve the existing ones.

I review new literature daily—new technologies, methods, and the latest research results on the diseases and targets I am working with. Sometimes this is part of the literature review for an ongoing project, but also regularly to keep myself on top of the latest scientific updates. Finally, I also try to be aware of the global circumstances that affect my field: new patented molecules, agreements between companies to develop new drugs, how computation (lately especially AI) is being used by other companies, which medical needs are highlighted in the press, etc.


What do you enjoy most about your job?

What I like most is that the job is very dynamic. You are always learning new things. Each project is different from the previous one. There are some techniques that you have to use regularly, but each project is a new challenge and to solve it you have to develop and use new methods or to learn how a new protein works, explore new chemical spaces … different challenges require different solutions and that makes each day different to the previous one. That is very rewarding.

Knowing that maybe some of the compounds I am designing can end up in the clinic helping to improve or solve some unmet medical problems, helping people to live better, is also very rewarding. I am conscious that most of my molecules will not arrive in the clinic, but the hope is always there and pushes me to go ahead.


Are there any aspects you would like to be different?

Not really. I am happy with my work as it is. What I like the least is the fact that computational results are sometimes underestimated. Some experimental scientists tend to consider computational results as irrelevant results; they do not believe in them. Things are changing and it must be said, this situation is less and less common, but it still exists.

The only other thing I would change is the experimental validation of my work, which should be faster. When you get interesting results and then send molecules to the lab to validate what you have observed, waiting until the results are ready is sometimes quite long. Or at least that is how it feels!


Why did you decide to move from academia to this job?

It was mainly due to stability and future perspectives. I didn’t want to be a nomad for many years, forcing my partner to leave her life to follow me. For a while, it might have been ok, but not for many years. During my Ph.D., I saw how over time, there was less funding, fewer openings, and it became more difficult to obtain a permanent position in academia. I realized the importance of having a good network of contacts. All this made me step away from my initial ambition of becoming a professor someday, and I decided to move to industry. And I didn’t regret my decision. I would do it again.

Luckily my day-to-day work has not changed too much from academia. And I like it a lot. The main change probably is that my research is directly applied to something. What I am doing will have an immediate impact, at least in my company. That is really rewarding.


Is there anything you miss from your time in the lab?

I miss the freedom of academic research, which can be triggered just by curiosity, just because you find something interesting. In industry, you can research interesting topics, but always with some clear goal in mind. Provide a service, develop a new tool, design a new drug, whatever. Your research usually needs to have a clear focus on something that is beneficial for the company. Sometimes research is motivated by curiosity, but that is unusual.


What has been challenging in your career and what is the hardest part of your job?

The most challenging part, probably, is to accept that you are going to fail. Several times. Most of the time. How many molecules reached the market? How many molecules arrived at clinical trials stage? Most of the molecules you find or design will not become “hits”, or if they are hits, they will fail to become “leads”. And without a lead, even pre-clinical trials are out of reach. Failure is hard and sometimes difficult to grapple with.

Working in a startup also had its own complications. I have experienced the rise and crash of a startup: A company that days before the announcement of its financial problems was considered a top national company in the field. I have seen how this company grew, and then in one day most of the workforce was fired. It is hard to live with that situation. The good moments are wonderful, but when something like that happens, it is hard.

However, people should not be scared of the startup world. I highly recommend working in a startup, as you can do a lot of different tasks and you can learn a lot of things not only related to your working field. However, you should be aware of the whole picture. In a startup, usually, you have more control and responsibilities than in a big company. However, after some years in the startup ecosystem, I am aware of the associated uncertainty. If certain goals cannot be achieved and the investors stop injecting money, that is it, you are out! And this can happen from one day to another.

If you are the CEO, things can be even more difficult. The problem is not only failing and losing a dream, something that you love and to which you have dedicated a lot of time. In Spain, most of the time, if a startup wants to get a loan from a bank as a company, the CEO has to assume the responsibility of the debt. If the company then crashes there are not just emotional consequences for the CEO, but also the associated legal and financial problems.

There are also difficulties in becoming a manager, as I was in my previous job. Nobody taught you how to manage people. You need to listen, understand the circumstances, be patient, and try to achieve a satisfactory solution for all parties if possible. Otherwise, sometimes you must impose what you believe is correct, and that is not easy as you know the working atmosphere can worsen, with the difficulties that it can imply. You need a deft touch and good interpersonal skills.


What advice would you give to students pursuing a job in this area?

My advice would be to follow your dreams rationally. If you know that you want to be a computational scientist in the pharma or biotech sector, that is ok, you can do it. But you need to know in which areas computation can be applied, which knowledge is required, and move in that direction.

There are lots of opportunities to take summer jobs in pharma and biotech companies working on small-molecule drug discovery. I would strongly recommend an internship in a company to see if you are a good fit for this kind of work.

I remember that during my Ph.D. I had a lot of unwarranted prejudices against research in industry. A short internship can help you to make your own experiences. Or if you do not want to do an internship, just be open-minded and believe that your daily work as a computational chemist in academia can be translated to industry almost identically.


Did you need to specialize in a certain field or is a general chemistry background sufficient?

You need to specialize. You need at least to know how to use computational chemistry programs, and how to dig into data.
Concretely, in my role, you would also need strong programming and data science knowledge, but depending on the position that is not always needed. In some roles, for instance, employers might prefer wider medicinal chemistry knowledge instead of programming.

Focusing on medicinal chemistry, cheminformatics (QSAR modeling, machine learning, data science, etc.) or computational chemistry (docking, molecular dynamics, quantum mechanics, etc.), is beneficial; however, experts in one field still need also some knowledge of the others.


Anything else you want our readers to know?

I would like to direct their attention to the importance of balancing work and personal life.

Often, joining a small company means that you will work on a lot of different things, and in fact, enjoy them. Being so involved makes you feel like the company is yours. If the industry (i.e., drug discovery) is something you are passionate about, things are even better. Altogether, this combination can make you work many hours without taking care of the work-life balance. But when the situation changes and suddenly you have more responsibilities, more work to do, more people to manage, you can feel overwhelmed.

It’s true that each person is different and can manage the same situation in totally different ways. But generally, I strongly believe that it is important to enforce limits. To know the main responsibilities of your position and if they are not clear, clarify them with your line manager. If the company grows or there is some internal reorganization and the responsibilities you had before are requiring too much time, it is necessary to stop, analyze the situation, and delegate some of your tasks to others.

There can be moments of stress, moments when you need to work too many hours, but this should not be a daily routine. It can happen from time to time, but not always. Having a good balance is important, and to be healthy is necessary to achieve an equilibrium. This advice applies not only to working in startups but to companies of any type and size, as well as to academia.

Melchor Sanchez-Martinez received an M.Sc. in biophysics from the University of Barcelona, Spain, in 2010, and an M.Sc. in theoretical and computational chemistry from the University Rovira I Virgili, Tarragona, Spain, in 2011. He received a Ph.D. in theoretical and computational chemistry from the University of Barcelona, Spain, in 2014. The same year he joined the startup Mind The Byte, Barcelona, Spain, as a computational chemist, and, in 2016, he was promoted to Scientific Director in the same company.

In December 2018, he left Mind The Byte to join Molomics, Barcelona, Spain, in March 2019 as Senior Scientific Researcher.


Selected Publications


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