It’s no secret that we’re in the ‘Information Age’. In the last decade, the number of online tools available to help students /researchers in STEM (and other fields) has grown enormously, something that is going to continue to grow in the years ahead.
The internet has made it possible to keep up with latest developments in modern medicine and allowed for more rapid dissemination of research. D. Cavalla wrote an excellent chapter in “The Practice of Medicinal Chemistry” on online resources. We recommend consulting that chapter for an extensive list of resources.1
Here, however, we review many instructive online tools dedicated to medicinal chemistry.
Let’s get started.
Useful Search Engines
eMolecules is an open-access chemical structure search engine where users can draw chemical structures under the “structure search” tab and upon completion of a search, a list of possible suppliers of the chemical of interest is provided. Alternatively, users may also use the “list search” feature to perform the search. eMolecules also provides information on the drawn structure’s molecular weight, molecular formula and its CAS Number, which is a unique numerical identifier assigned to all known chemical substances in the open scientific literature (example: fluoxetine).
For looking up scholarly articles, Google Scholar is a free alternative to the likes of Scopus and Scifinder. Most research articles have a unique identifier known as Digital object identifier (DOI) and articles can be easily retrieved by inputting the DOI. Full access to articles may require users to be subscribers of article publishers, but if you are part of an academic institution, there’s a high chance that your institute is a subscriber. Some scholarly articles are open-access, meaning they are freely available.
Useful Scientific Journals for Medicinal Chemistry Students
|Journal of Medicinal Chemistry||American Chemical Society|
|ACS Medicinal Chemistry Letters||American Chemical Society|
|Mini-Reviews in Medicinal Chemistry||Bentham Science Publishers|
|Bioorganic & Medicinal Chemistry||Elsevier|
|Drug Discovery Today||Elsevier|
|European Journal of Medicinal Chemistry||Elsevier|
|Nature Reviews Drug Discovery||Nature Publishing Group|
For a more comprehensive list, see this search result from SCIMago which also includes journals for pharmacology students.
OMICtools is an online directory for finding software and computational tools related to genomics, transcriptomics, proteomics and metabolomics. There are currently more than 4400 tools in OMICtools.
ChemSpider, which is owned by the Royal Society of Chemistry (RSC), is a free database of chemicals. ChemSpider sources information from hundreds of data sources and has data on more than 67 million molecules. Upon completion of a search, ChemSpider provides information such as structural information and chemical properties (See triclabendazole below).
Aside: Triclabendazole, which was recently approved by the US FDA (13-Feb-2019), is an anthelmintic drug used to treat fascioliasis.
Drug Metabolism Question:
Based on the structure of triclabendazole, propose possible metabolism products.
PubChem is a database of chemicals at the National Institutes of Health (NIH) of the USA where biological data on chemical compounds are collated and archived into the database. Currently, PubChem contains the largest collection of publicly available chemical information with more than 100 million substances in that database.
The US FDA has a list of databases useful to medicinal chemists.
DrugBank is a free online database that compiles information on drugs / drug targets, including pharmacokinetic, pharmacological, chemical and pharmaceutical data. There are currently more than 11,900 drug entries in DrugBank.
Spectral Database for Organic Compounds (SDBS)
Particularly useful for synthetic medicinal chemists, SDBS is a free searchable database of spectroscopic data for ~34,000 organic molecules. SDBS includes data for six characterisation techniques used in chemistry – 1H nuclear magnetic resonance (1H-NMR),13C nuclear magnetic resonance (13C-NMR),laser Raman, electron ionisation mass (EI-MS), Fourier-transform infrared (FT-IR) and electron paramagnetic resonance (EPR) spectra. Users may input CAS numbers to find spectroscopic information on the organic molecule of interest. SDBS is available in both English and Japanese.
Human Metabolome Database (HMDB)
HMDB is a free metabolomics database created by the Human Metabolome Project funded by Genome Canada. HMDB, which has more than 114,000 metabolite entries, contains or links three kinds of data: clinical, chemical and molecular biology/biochemistry data.
Some Useful Applications/Software
Pred-hERG is a free computational tool for predicting cardiotoxicity based on statistically significant and externally predictive QSAR models of hERG blockage. We discussed QSAR and Pred-hERG in more detail here.
XenoSite Web allows users to perform pharmacokinetic predictions of human in vivo metabolism and reactivity of small molecules. For performing predictionism, XenoSite Web accepts inputs such as the Simplified molecular-input line-entry system (SMILES) notation for molecules, which can be obtained from PubChem or ChemSpider.
Research Opportunities for Medicinal Chemistry Students:
If you are a student, who is an aspiring researcher or someone who wishes to move to another position, here are some platforms you may find useful:
EURAXESS is a platform where researchers can find information on research opportunities as well as more detail on the current research climate in Europe. EU citizens do not require work permits to work and settle anywhere in the EU. For those who are non-EU citizens, information on visa requirements and working permits can also be found.
Nature Careers is a dedicated webpage for advertising available positions for candidates in science.
Often, research opportunities are advertised on the social networking site, LinkedIn.
Phase 1 Biotransformation:
Oxidation to sulfone and sulfoxide metabolites.
(1) Cavalla, D. Chapter 35: Web Alert: Using the Internet for Medicinal Chemistry. In The Practice of Medicinal Chemistry; Wermuth, C. G., Aldous, D., Raboisson, P., Rognan, D., Eds.; Elsevier Ltd.: San Diego, CA, USA, 2015.