Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 80 /hr

★★★★★

☆☆☆☆☆

Hire Dr. Vaclav N.

Vietnam

USD 80 /hr

Scientific Consulting, Medicinal & Organic Chemistry, Induced Proximity, Early Drug Discovery, CRO & Project Management

Profile Summary

Hi, I am Václav, founder of Ambrosigen and scientist at heart. (https://ambrosigen.com) I am keen to connect, collaborate, and discuss science or any topics we might have in common! My core expertise lies in organic synthesis and medicinal chemistry. I enjoy the intellectual challenge of deconstructing complex biological and chemistry problems into efficient solutions. Over my career, I have worked on diverse research projects in four different countries (Germany, UK, France, Czech Rep.), spanning early drug discovery, chemical biology, synthetic chemistry and establishment of chemogenomic library. At the Structural Genomics Consortium (SGC), I led a team of medicinal chemists and coordinated interdisciplinary projects at the interface of industry and academia, collaborating with institutions such as University of Oxford, University of Toronto, Karolinska Institute, ETH Zurich, as well as biotech and pharma companies (e.g. Merck, Pfizer, BI, Neosphere, Promega). This equipped me with the ability to understand not only chemistry but also related biological disciplines and navigate the complexity of large organisations and projects. Over my career, I was involved in numerous projects focused on the development of novel degraders (PROTACs), and E3 ligase ligands. Together with my team at SGC we developed, for instance, the first-in-class PROTAC degrader targeting CK1δ/ε, the first-in-class small-molecule ligand for E3 ligase TRIM7, and a workflow for evaluating E3 ligases and their ligands for their utility in targeted protein degradation. In addition, I gained expertise in the development of biologically active small molecules targeting, protein kinases (e.g. CLKs, HIPKs, ALK1/2, CK1), epigenetic targets (e.g. WDR5), transmembrane receptors (Smoothened) or human telomerase reverse transcriptase (hTERT) and other biological targets. Beyond medicinal chemistry, I gained also experience with total synthesis of natural products, chemo-enzymatic synthesis of carbohydrate chains and handling mammalian cell cultures. Some of my significant contributions include the development of high-quality chemical probes (e.g. LH168, MU1210, MU1742, MU1920) that became commercially available and are widely used by the community. Among these we identified for instance highly selective ALK1/2 chemical probe MU1700 exhibiting favorable PK/PD profile and extraordinary brain penetration. Moreover, I led the chemistry efforts that yielded best-in-class CK1 inhibitors which resulted in identification of preclinical candidate and the establishment of a spin-out company.

Subject Matter Expertise

• ☆ Chemical Reagent Development
• ☆ Natural Product Chemistry
• ☆ Organic Chemistry
• ☆ Biotechnology & Bioengineering
• ☆ Chemical Biology
• ☆ Drug Discovery
• ☆ High Throughput Screening (HTS)
• ☆ Drug Target Identification
• ☆ Hit-to-Lead & Lead Optimization
• ☆ Medicinal Chemistry
• ☆ Drug Design
• ☆ Combinatorial Chemistry
• ☆ Structure-Activity Relationship (SAR) Studies
• ☆ Project Management

Services

• Writing
• Research
• Consulting

Writing Technical Writing, Copywriting, General Proofreading & Editing

Research Feasibility Study, Technology Scouting, Fact Checking, Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Work Experience

Goethe University Frankfurt

December 2020 - Present

Team Leader - Medicinal Chemistry

Structural Genomic Consortium

September 2020 - April 2025

Education

Bc., Msc., PhD (Department of Chemistry)

Masarykova univerzita

- Present

Certifications

• IBM Professional Project Management Certificate

  IBM

  June 2025 - Present

Publications

JOURNAL ARTICLE

Lasse Hoffmann, Christopher Lenz, Frederic Farges, Serah W. Kimani, Johannes Dopfer, Sabrina Keller, Martin Peter Schwalm, Hanna Holzmann, Andreas Kraemer, Aiping Dong, et al. (2025). Discovery of an exquisitely selective WDR5 chemical probe accelerated by a high-quality DEL–ML Hit . RSC Chemical Biology.

Nebojša Miletić, Janik Weckesser, Thorsten Mosler, Rajeshwari Rathore, Marina E. Hoffmann, Paul Gehrtz, Sarah Schlesiger, Ingo V. Hartung, Nicola Berner, Stephanie Wilhelm, et al. (2025). Workflow for E3 Ligase Ligand Validation for PROTAC Development . ACS Chemical Biology.

Adrian Haag, Václav Němec, Pavlína Janovská, Jana Bartošíková, Bikash Adhikari, Juliane Müller, Martin P. Schwalm, Štěpán Čada, Uli Ohmayer, Henrik Daub, et al. (2024). Development and Discovery of a Selective Degrader of Casein Kinases 1 δ/ε . Journal of Medicinal Chemistry.

Václav Němec, Marek Remeš, Petr Beňovský, Michael C. Böck, Eliška Šranková, Jong Fu Wong, Julien Cros, Eleanor Williams, Lap Hang Tse, David Smil, et al. (2024). Discovery of Two Highly Selective Structurally Orthogonal Chemical Probes for Activin Receptor-like Kinases 1 and 2 . Journal of Medicinal Chemistry.

Christian J. Muñoz Sosa, Christopher Lenz, Anton Hamann, Frederic Farges, Johannes Dopfer, Andreas Krämer, Veronika Cherkashyna, Andrey Tarnovskiy, Yurii S. Moroz, Ewgenij Proschak, et al. (2024). A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7 . ACS Chemical Biology.

Václav Němec, Prashant Khirsariya, Pavlína Janovská, Paula Martín Moyano, Lukáš Maier, Petra Procházková, Pavlína Kebková, Tomáš Gybel', Benedict‐Tilman Berger, Apirat Chaikuad, et al. (2023). Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity . Angewandte Chemie International Edition.

Václav Němec, Martin P. Schwalm, Susanne Müller, Stefan Knapp(2022). PROTAC degraders as chemical probes for studying target biology and target validation . Chemical Society Reviews. 51. (18). p. 7971--7993. Royal Society of Chemistry ({RSC})

Rodrigo A. Gama-Brambila and Jie Chen and Yasamin Dabiri and Georg Tascher and V{\'{a}}clav N{\v{e}}mec and Christian Münch and Guangqi Song and Stefan Knapp and Xinlai Cheng(2021). A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins . JACS Au. 1. (6). p. 777--785. American Chemical Society ({ACS})

V{\'{a}}clav N{\v{e}}mec and Luk{\'{a}}{\v{s}} Maier and Benedict-Tilman Berger and Apirat Chaikuad and Stanislav Dr{\'{a}}pela and Karel Sou{\v{c}}ek and Stefan Knapp and Kamil Paruch(2021). Highly selective inhibitors of protein kinases CLK and HIPK with the furo[3,2-b]pyridine core . European Journal of Medicinal Chemistry. 215. p. 113299. Elsevier {BV}

Paula Mart{\'{\i}}n Moyano and V{\'{a}}clav N{\v{e}}mec and Kamil Paruch(2020). Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential . International Journal of Molecular Sciences. 21. (20). p. 7549. {MDPI} {AG}

V{\'{a}}clav N{\v{e}}mec and Michaela Hylsov{\'{a}} and Luk{\'{a}}{\v{s}} Maier and Jana Flegel and Sonja Sievers and Slava Ziegler and Martin Schröder and Benedict-Tilman Berger and Apirat Chaikuad and Barbora Val{\v{c}}{\'{\i}}kov{\'{a}} and Stjepan Uldrijan and Stanislav Dr{\'{a}}pela and Karel Sou{\v{c}}ek and Herbert Waldmann and Stefan Knapp and Kamil Paruch(2019). Furo[3,2‐b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway . Angewandte Chemie International Edition. 58. (4). p. 1062--1066. Wiley

Mariana Amaro and Jan Brezovsk{\'{y}} and Silvia Kov{\'{a}}{\v{c}}ov{\'{a}} and Jan S{\'{y}}kora and David Bedn{\'{a}}{\v{r}} and V{\'{a}}clav N{\v{e}}mec and Veronika Li{\v{s}}kov{\'{a}} and Nagendra Prasad Kurumbang and Koen Beerens and Radka Chaloupkov{\'{a}} and Kamil Paruch and Martin Hof and Ji{\v{r}}{\'{\i}} Damborsk{\'{y}}(2015). Site-Specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence . Journal of the American Chemical Society. 137. (15). p. 4988--4992. American Chemical Society ({ACS})

BOOK CHAPTER

Václav Němec, Stefan Knapp (2023). Quality Control of Chemogenomic Library Using LC-MS . Methods in Molecular Biology.

DISSERTATION THESIS

Václav Němec(2020). DISCOVERY OF NOVEL SELECTIVE MODULATORS OF SELECTED THERAPEUTICALLY RELEVANT BIOLOGICAL TARGETS . Unpublished. Unpublished

PATENT

4—(1h— imidazol— 5— yl) -1h-pyrrolo [2, 3-b] pyridines for use in the treatment of leukaemias, lymphomas and solid tumors.

Furopyridines as inhibitors of protein kinases.

Václav Němec Substituted furopyridines for therapeutic use.