Akash Mitra

Bioinformatics – A double-edged sword

The fundamental essence of being a biologist (for me being a student of Microbiology) is the fact that we get to deal with live lab-works and experiments hands on. To be honest, it is really fun spending time in the lab rather than sitting in a classroom attending a lecture.

Now, when you are a University student and you are performing lab works for the course you are enrolled in, then most of the time the situation is an ideal one i.e. you have all the reagents, instruments etc. in proper order which have already been supervised by your professor in-charge. On the contrary, if you are working on projects that are being funded by some funding agencies, there are a couple of things that you need to consider before you jump on with the experiments. Firstly, the agency that is funding your research is doing so because it recognizes the potential in your work and hence, you become answerable to them at a professional level. They would provide a window of time and they would be expecting some progress in your research just to make sure that their decision of funding did not go down the drain. Now, holding on to this thought you can make out the second constrain, which is this caveat of expenses that you need to keep in mind before any lab-work is performed. The decisions made by you while you are purchasing chemicals, reagents and utilities is dictated by the type of work you perform and adding to that, you do not have unlimited inflow of funds.

Now, here lies the witty utilization of the profound arsenal of tools provided by computational biology i.e. bioinformatics. Let’s say for example, when the pandemic had hit in 2020, the scientists all around the world were rattling their brains out for a cure against the new virus. Since it was a state of emergency, primarily the scientists turned to “repurposing of old drugs” which had already shown fruitful effects against similar viruses in the past. FYI, “repurposing” refers to using existing drugs with slight modifications that might seem fit. Now, chemical synthesis of drugs is very time taking and expensive, and if the scientists would have immediately turned to synthesizing new drugs and moreover, if it would have failed the human trials, then there would be millions of dollars burnt for no good reason. In these situations (pandemic or not) to save time and money people always go for virtual screening of drugs before synthesizing them chemically. The repurposing is performed using various computer programs and a virtual model is created for the drug. Then the drug is made to interact with the target, again virtually. If the results are promising, then the chemical synthesis is undertaken otherwise further virtual modifications are performed.

Apart from drug designing, there can be other applications as well. Let’s say, you isolate a brand new microbe which hasn’t been reported before. Before going to the lab and characterizing it using some wet lab hit and trial, initially you can take out the sequence of DNA and scavenge various online databases that might have some organisms with similar sequences. Over there you might find something that is similar to your query and since it is in the database, you might expect to find some literature related to the characterization. With this, you get to narrow down the probabilities and step into a specific realm where you explore the reported techniques to your new microbe. That would eventually in the long run save your money, time and most importantly you don’t have to start from a blank page anymore which otherwise would have been quite scary.

So, in conclusion, you may consider computational biology as a double edged sword. On one hand, you take a step forward to your research goal and on the other hand, you take that step without spending a lot of your time, money and, effort. Hence, dipping your hands into the pool of bioinformatics can keep you ready with some tricks up your sleeves at all times.

PS, I posted a video on YouTube titled “Protein-ligand docking using PyRx” which deals with a software called PyRx which is used to screen drugs virtually. Do consider checking it out. You might get to learn a new skill.

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