BAGIM is an active community of Boston area scientists bringing together people from diverse fields of modeling and informatics to impact life and health sciences. BAGIM strives to create a forum for great scientific discussions covering a wide range of topics including data management, visualization, computational chemistry, drug discovery, protein structure, molecular modeling, structure-based drug design, data mining, software tools, and the sharing of goals and experiences. Our community is made up of participants from academia, government, and industry whose goal is to engage in the discussion of science involving a synthesis of theory and technology. Discussions sponsored by BAGIM are targeted to the needs and interests of informatics scientists, computational chemists, medicinal chemists, and statisticians. BAGIM also provides opportunities for networking within these disciplines as well as an arena for the dissemination of information of specific interest to the membership.

Friday, December 8, 2023

Marcus Gastreich — The 0D to 3D Journey in On-Demand Chemical Space 

 We are hosting a December BAGIM in-person event with BioSolveIT. We welcome Marcus Gastreich with the presentation Towards the Uncountable — The 0D to 3D Journey in On-Demand Chemical Space

Date: December 5, 2023 @ 6:00 PM

Location: Nimbus Therapeutics, 22 Boston Wharf Road, Floor 9
Boston, MA 02210 USA

5:45 PM - Registration / Sign-in
6:00 PM - 7:00 PM - Presentation & Q&A
7:00 PM - 9:00 PM - Reception / Social Gathering with Food & Drink

Please arrive early to get checked in. We will hosting a social networking event after the presentation.

Host: BAGIM & BioSolveIT

Speaker: Marcus Gastreich, SVP Application Science, BioSolveIT


2017 was the beginning of a groundbreaking collaboration. Enamine, a Ukrainian compound manufacturer, joined forces with BioSolveIT to pioneer what would soon become the world's most sophisticated journey in the expansive multi-trillion chemical space.

Since that time, not only has the core of Enamine's REAL concept expanded at an exponential rate (with other compound providers quickly joining the movement), but the computational tools designed to explore these vast molecular realms have also seen remarkable enhancements.

Collectively, compound providers now showcase nearly 8 trillion on-demand molecules. The "smaller" among these sets, referred to as "ultra-large libraries," can be probed using specialized software like Arthor, or even docked with DOCK5. However, these enumeration-based techniques are nearing their limits, especially with libraries extending beyond several tens of billions.

Our focus is on sidestepping enumeration methods as much as possible. This shift in thought has propelled drug research into domains previously deemed unreachable, exploring molecular sizes well beyond the trillions — all achievable on modest computer setups, delivering results within seconds for standard small molecule queries.

This presentation will delve into the latest topics:

  • The coordinate-free "0D" FTrees algorithm, for rescaffolding.
  • Distinctive 2D algorithms, rooted in Tanimoto-like metrics.
  • 3D methods, exemplified by Chemical Space Docking and Fragment Growing.

These innovative techniques have undergone preliminary tests, or were co-developed in partnership with pharmaceutical entities. As a result, we have early applications and real-world success narratives to share. Of course, we won't shy away from discussing hurdles either.

The presentation will allow ample time for an in-depth Q&A session.


Enamine. Enamine REAL Space and REAL Database. https://enamine.net/index.php?option=com_content&task=view&id=254 (2021).

Warr, W. A., Nicklaus, M. C., Nicolaou, C. A. & Rarey, M. Exploration of Ultralarge Compound Collections for Drug Discovery. J. Chem. Inf. Model. 62, 2021–2034 (2022).

Korn, M., Ehrt, C., Ruggiu, F., Gastreich, M. & Rarey, M. Navigating large chemical spaces in early-phase drug discovery. Curr. Opin. Struct. Biol. 80, 102578 (2023).

Arthor 3.0, NextMove Software, Inc.: Cambridge, UK, 2020.

Lyu, J. et al. Ultra-large library docking for discovering new chemotypes. Nature 566, 224–229 (2019).

Hoffmann, T. & Gastreich, M. The next level in chemical space navigation: going far beyond enumerable compound libraries. Drug Discov. Today 24, 1148–1156 (2019).

BioSolveIT GmbH. infiniSee. (2023).

Bellmann, L., Penner, P. & Rarey, M. Topological Similarity Search in Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. 61, 238–251 (2021).

Beroza, P. et al. Chemical Space Docking Finds Novel ROCK1 Kinase Inhibitors by Large-Scale Structure-Based Virtual Screening. Nat. Commun. 13, (2022).

Penner, P., Rarey, M., Gastreich, M. et al. FastGrow : On-the-fly growing and its application to DYRK1A. J Comput Aided Mol Des 36, 639–651 (2022).

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