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CLC Bio Enters Drug Discovery Software Market with Molegro Acquisition

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Stepping away from its focus on sequence analysis, CLC Bio officially threw its hat into the drug discovery software ring with its acquisition of Molegro, a developer of molecular modeling software.

The purchase, announced this week, marks the first acquisition for CLC Bio. Both firms are privately held and based in Aarhus, Denmark.

The acquisition expands CLC's portfolio beyond its existing fleet of NGS analysis software — which includes CLC Genomics Workbench and Genomics Server —to add tools for molecular docking, including prediction and analysis of protein-ligand interactions, screening of compound databases for activity against receptors, and determination of molecule similarity.

Under the terms of the acquisition, all existing Molegro customers with active support and software upgrade contracts have been transferred to CLC Bio and all of Molegro’s staff are relocating to CLC Bio’s headquarters.

Lasse Gorlitz, CLC Bio’s vice president of communications, told BioInform that the purchase aligns with the company's strategy to provide tools that encompass all aspects of molecular analysis.

“Right now, we are really focused on next-generation sequencing and [Molegro] is in a different area of the spectrum of molecular analysis with a focus on proteins and ligands … [so] it's some distance away from the core of our current product portfolio,” he said. “The idea is to start building from both ends and then eventually we’ll have something that is coherent across the whole spectrum.”

Developing these types of tools in house would have taken a great deal of time, so CLC opted to buy rather than build. Molegro was an appealing target because it offers “really high-quality software that we think meets our standards," Gorlitz said, adding that CLC will also benefit from bringing Molegro's developers on board.

For Molegro, it “allows us to become part of a strong analysis platform and focus even more on developing the next generation of molecular docking products," René Thomsen, the company’s CEO, said in a statement.

Other advantages of the acquisition include access to a much larger client base and more development resources as well as a presence in the North American market, Thomsen told BioInform.

It also shifts the burden of providing software support to the shoulders of a much larger team at CLC Bio, freeing Molegro’s employees to focus on software development, Gorlitz said.

Molegro opened its doors in 2005, with funding from unnamed investors to commercialize algorithms developed by Thomsen during his days as a doctoral student at Aarhus University.

The company currently offers four products for drug discovery. Its flagship product is the Molegro Virtual Docker, which is a platform for predicting protein-ligand interactions.

The software uses the MolDock docking engine, which is based on “a heuristic search algorithm that combines differential evolution with a cavity prediction algorithm,” according to a paper describing the method published in 2006 in the Journal of Medicinal Chemistry.

According to the authors, in comparison tests with other docking programs such as Schrödinger’s Glide and Tripos’ Surflex-Dock, the MolDock algorithm provided more accurate results than its competition — MVD was able to identify the correct binding model of 87 percent of protein-ligand complexes while Glide and Surflex had about 82 percent and 75 percent accuracy, respectively.

Other tools in the company’s suite include Molegro Molecular Viewer, which is a free application for visualizing protein-ligands and results from MVD; Molegro Data Modeller, which is used for data modeling, mining, and visualization; and Molegro Virtual Grid, which provides infrastructure for distributing docking runs across multiple machines.

The tools have been used in a number of drug discovery projects, including several focused on designing inhibitors that could be used to treat bacterial infections and others investigating potential antimalarial agents.

The company has different licensing schemes for academic and commercial groups, Thomsen said. He declined to divulge specific figures but said that the cost depends on factors such as the number of licensees, and that it is in the same ballpark as prices for competing products.

Potential competitors for Molegro’s products include offerings from companies like Schrödinger and Tripos as well as Accelrys and University of Washington’s Rosetta software, which is now available as a cloud-based solution as a result of a partnership with Seattle-based Insilicos (see related story this issue).

Thomsen believes that Molegro’s tools are easier to use and more accurate than the competition, which gives the firm the edge it needs to stay ahead in the drug discovery space. For example, MVD’s solutions work on Linux, Windows, and Mac systems and are easy to deploy and use while some competing products are restricted to single operating systems and require command-line knowledge, he said.

Additionally, Molegro’s tools offer features that it claims aren’t available from competitors. This includes things like hybrid docking, which allows users to incorporate prior knowledge of candidate drug molecules into docking simulations to improve results, Thomsen said. The software can also make use of graphics processing units to speed up docking while maintaining accuracy, he said.

CLC Bio said that it intends to invest "significant resources" in developing Molegro’s protein-ligand docking and data modeling software. Along these lines, it plans to release updated versions of Molegro’s software in the next few months.

These updates will include applications that let users inspect the results of their docking activities in greater detail so that they can home in on aspects that need further refinement, as well as visualization tools that display chemical interactions in proteins and the effects of these interactions, Molegro’s Thomsen told BioInform.

The updated software will also make it possible for users to distribute docking runs to multiple central processing units among other features that will also improve performance, he said.

For now, CLC Bio will offer Molegro’s software as separately branded products although the company intends to merge features from the molecular modeling software into its existing portfolio and could make these updated tools available as early as next year, Gorlitz said.

Molegro will continue to market its software through existing reseller agreements with several external companies as well as through CLC Bio’s sales channels, Thomsen said.

Current distributors of Molegro’s software include the Northern Science Consulting group, which handles software distribution in Japan and Korea; AH Systems Group and Red eQuus, which handle sales in US and Canada, respectively; PIC Informática, which manages the market in Brazil; and Chemcad and GMSL, which support clients in France and Italy, respectively.

Meanwhile, Scientific Software Solutions manages sales in Greece and Cyprus; Beijing Hongcam Software Technologies and TurnTech handle sales in the Chinese market; Tri-I Biotech is the current distributor for Taiwan; and Achema handles sales in Singapore, Indonesia, Malaysia, and Thailand.

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