The CNPEM’s computational biology group has created a free online service to help researchers search for, categorize, and select drug bonding sites on proteins
Researchers at the Brazilian Center for Research in Energy and Materials (CNPEM) have just created an online service called KVFinder-web. This online resource is offered to the academic community and the general public and allows users to view and classify cavities in proteins as well as other types of molecules. This new tool can aid research in various knowledge areas.
The study that led to the development of this online tool was published in May in Nucleic Acids Research. Another article by the computational biology group at the CNPEM, in collaboration with the Université Toulouse III─Paul Sabatier in France, was featured the following month on the cover of JCIM, the Journal of Chemical Information and Modeling.
The cover article described the unexpected use of the program for a structure that was completely unrelated to a protein; this alternative use was intended to identify and quantify the interior dimensions of artificial structures known as “supramolecular cages” which are generally composed of multiple carbon atoms. These cages are used to isolate, host, or capture molecules in chemical reactions for a variety of purposes, such as encapsulating hazardous or explosive byproducts during the process of synthesizing a chemical compound.
KVFinder can successfully determine the space within supramolecular cages. Once the volume and aperture are known, researchers can decide whether it is worthwhile to synthesize the molecule, for example. The study shows how software of this type can be used for various purposes and is still underutilized.
Even though KVFinder can analyze the surface of any molecule and identify and describe any cavities it may have, this type of tool was initially considered for the study of macromolecules, principally proteins.
This is because we have known for some time that the spaces inside a protein are important to its functionality. These spaces are formed when the molecule folds into itself and offer binding sites; in other words, if the protein is a virus spike, there is a good chance that the virus molecules that interact with cell membranes and/or antiviral medications will be located within one of these cavities.
This is also true for all types of enzymes. For many enzymatic proteins (like chinases, for example), it is widely known that the deepest cavity is generally the catalytic one.
The famous lock-and-key hypothesis derived from one of the first studies on the enzyme/substrate complex conducted by Emil Fischer in 1894. Today this analysis is considered too simplistic for the various circumstances involving chemical reactions and the profiles of the molecules involved, but cavities are still important in biochemical and pharmacological processes.
According to Paulo Oliveira, who coordinated the computational biology group at the CNPEM, even though the relationship between protein shape and function has been known for some time, there was a problem with the method and a need for an effective tool to analyze protein cavities that offered better predictions of the phenomena that depend on their spatial geometry.
KVFinder-web, step by step
The KVFinder-web tool is relatively easy to use: just upload the molecular structure file in PDB format or insert the 4-digit code and select the visualizations of interest, and the results appear in a few seconds.
Many of the researchers who work with proteins are familiar with the PDB format and the worldwide protein data bank. If a molecule has not yet been included in the data bank, its detailed structure can be obtained from AlphaFold or other modeling programs and uploaded to KVFinder-web.
Once the uploaded file is processed, the page shows a preliminary view of the spatial structure of the molecule and the options for viewing cavity characteristics such as volume, depth, and hydrophilia. A large number of files (for different molecules) can be uploaded at the same time, and the analysis can be organized according to the cavity properties. With this combination of geometric and physical/chemical data, researchers can more efficiently infer which binding molecule (like a pharmaceutical, for example) might be most appropriate for testing.
The visualizations provided by KVFinder-web allow “atomic and spatial perspectives to complement each other and supplement the search for binders of interest, which previously was difficult to study,” says João Victor Guerra, author of the article for the launch of the platform.
This is not the first time a computer program has been developed to view the surface of molecules, but it is the first time such a comprehensive service is available online. Additionally, KVFinder-web is the entryway to a platform containing software previously released by the CNPEM which have now been updated. Guerra notes that the online interface makes the platform easier and more appealing to users who may not have much experience in the area.
Besides improved accessibility, one of the main differentials of this tool lies in the effective demarcation of subtle characteristics on the surface of the molecule that similar programs from other institutions are not able to detect.
For example, in the case of larger cavities composed of multiple spaces or gaps that differ from each other, the few software tools available prior to the new online platform were only able to recognize the overall space in an approximate and general manner. But KVFinder-web identifies not only the overall cavity but also the small gaps within it, and provides relevant information about each individual space.
In describing further challenges involved in adapting to the reality of molecules in creating surface analysis software, the authors of the article also cited the constant and active movement of proteins in space (and consequent changes in their shape and surface, especially when they interact with the substrate), as well as execution of the program on a large scale. This happens during comparative analysis of various proteins at the same time, for example, to find a certain suitable pharmaceutical, or in order to analyze and organize the results for molecules from an entire microbiome instead of investigating one species at a time.
In these cases, optimizing the algorithms made for the current platform and selecting the visualizations from the online service offers solutions. What makes this group of programs special is the combination of all the new capabilities and the ground-breaking nature of the online interface.
There are many potential applications for the new online tool: possibilities have already been demonstrated (in the case of the supramolecular cages) in research arenas beyond virology, biochemistry, and pharmacology. Besides using the online access, university professors can also download and install KVFinder-web on their institution’s server and use it in the classroom. Finally, the researcher Paulo Oliveira mentions another interesting aspect of use by the scientific community: “even if it isn’t the main focus of their research, sometimes users just want to see what the protein they are working with looks like, which is always fascinating, and the online services allows them to do this.”.
A sophisticated and effervescent environment for research and development, unique in Brazil and present in few scientific centers in the world, the Brazilian Center for Research in Energy and Materials (CNPEM) is a private non-profit organization, under the supervision of the Ministry of Science, Technology and Innovation (MCTI). The Center operates four National Laboratories and is the birthplace of the most complex project in Brazilian science – Sirius – one of the most advanced synchrotron light sources in the world. CNPEM brings together highly specialized multi-thematic teams, globally competitive laboratory infrastructures open to the scientific community, strategic lines of investigation, innovative projects in partnership with the productive sector and training of researchers and students. The Center is an environment driven by the search for solutions with impact in the areas of Health, Energy and Renewable Materials, Agro-environment, and Quantum Technologies. As of 2022, with the support of the Ministry of Education (MEC), CNPEM expanded its activities with the opening of the Ilum School of Science. The interdisciplinary higher course in Science, Technology and Innovation adopts innovative proposals with the aim of offering excellent, free, full-time training with immersion in the CNPEM research environment. Through the CNPEM 360 Platform, it is possible to explore, in a virtual and immersive way, the main environments and activities of the Center, visit: https://pages.cnpem.br/cnpem360/.