Periodic Reporting for period 2 - AEGIS (Accelerated Early staGe drug diScovery)
Periodo di rendicontazione: 2018-01-01 al 2019-12-31
The development of potent and safe new drugs - especially for rare and neglected diseases - is one of the biggest challenges of the upcoming decades, as shown by many recurring epidemics, including the current COVID19 pandemic. The aim of the AEGIS ITN was to implement a unique comprehensive, cross-disciplinary, intersectorial and structured curriculum for PhD students in the European Research Area by establishing an integrated training platform for the next generation of European researchers in early drug discovery. Important added value was provided through networking with European pharmaceutical companies. A main research goal of AEGIS was improving the efficiency and success of early stage drug development by combining innovative methods and techniques. This should allow to tackle novel promising but challenging targets (i.e. protein-protein interactions), which are often neglected due to the high risk associated with their validation. The overall aims of the AEGIS project were:
Aim 1: Train a new generation of researchers in integrated structure-based drug discovery in an open innovation collaboration between academic and industrial partners for enhancing their employability
Aim 2: Offer ESRs access to world-class expertise and infrastructure in an intersectorial and multidisciplinary research environment
Aim 3: Accelerate and improve early drug discovery by developing novel methods
Aim 4: Identify lead compounds for targets involved in rare and neglected diseases of urgent medical need
Aim 5: Form a sustainable network of academic and industrial drug discovery centers of excellence and ESRs that will last beyond the AEGIS timeline.
AEGIS researchers were effectively trained and now contribute to a highly skilled workforce for Europe that will multiply as they will pass on their experience and integrative training to their working environments in academia and industry. AEGIS was an important factor for the career development of its young researchers (many already found attractive jobs in academia, biotech and pharmaceutical industry), thereby promoting a sustainable development in innovative drug discovery, in particular for rare and neglected diseases.
Aim 1: Train a new generation of researchers in integrated structure-based drug discovery in an open innovation collaboration between academic and industrial partners for enhancing their employability
Aim 2: Offer ESRs access to world-class expertise and infrastructure in an intersectorial and multidisciplinary research environment
Aim 3: Accelerate and improve early drug discovery by developing novel methods
Aim 4: Identify lead compounds for targets involved in rare and neglected diseases of urgent medical need
Aim 5: Form a sustainable network of academic and industrial drug discovery centers of excellence and ESRs that will last beyond the AEGIS timeline.
AEGIS researchers were effectively trained and now contribute to a highly skilled workforce for Europe that will multiply as they will pass on their experience and integrative training to their working environments in academia and industry. AEGIS was an important factor for the career development of its young researchers (many already found attractive jobs in academia, biotech and pharmaceutical industry), thereby promoting a sustainable development in innovative drug discovery, in particular for rare and neglected diseases.
INNOVATIVE APPROACHES TO DRUG DISCOVERY
Screening results for active fragments were analysed for their ability to induce new pockets and interact with transient features in the protein binding interfaces. Novel methods to validate and identify fragment binding poses using paramagnetic NMR, including the development of novel paramagnetic lanthanide binding tags, were developed and demonstrated with AEGIS targets. We implemented novel methods using NMR and molecular dynamics simulations for the detection and utilization of transient pockets with exciting promising results. Pharmacophore models used for computational screening were complemented with transient features detected by molecular dynamics. X-ray fragment screening was performed and structural biology information obtained was used to guide synthesis steps for medicinal chemistry optimization. A comparative analysis of the NMR and X-ray fragment screens, regarding type and quantity of hits was performed and highlighted interesting complementarities.
EXPERIMENTAL SCREENING AND STRUCTURAL BIOLOGY
A number of promising target proteins were selected for in-depth fragment-based lead discovery: T. cruzi PEX14, FPPS and Mycobacterium protein-tyrosine phosphatase (MptpB), UMP kinase (UMPK) and 14-3-3/p53. Feasibility studies were performed with well-established model systems. Furthermore, several virtual screening hits were characterized by NMR as binders and co-crystallized with PEX14 driving the protein in alternative crystal packing. The crystallization of FPPS, MptpB and UMPK was optimized, cryo-EM single particle structural analysis was performed for large target proteins. A fragment screening at AZ using 14-3-3/p53 and the AZ fragment library resulted in two fragment hits, which were further evolved by chemical synthesis.
MEDICINAL CHEMISTRY
A fragment library was designed based on multicomponent reaction (MCR) principles and physically realized with currently >700 fragment compounds plated. The physical fragment library is available to every member of the AEGIS consortium for screening purposes. Several hits in different projects were found. Hits generated by other screening methods were taken up and optimised by medicinal chemistry methods.
COMPUTATIONAL ANALYSIS (WP4)
Computational approaches focused on the identification and design of inhibitors with therapeutic potential. Computational analysis connects the hit and lead finding activities through virtual screening, molecular design (“scaffold hoppig”), fragment library design and reaction, generation of SAR models, investigation of novel effector mechanisms exploiting original computational methods, including molecular dynamics (MD) and transitional functional mechanism modelling. Excellent results were obtained regarding these objectives: novel inhibitors were derived for various AEGIS targets, which were validated and further developed using experimental methods. New computational methods were implemented for fast and efficient analysis of NMR-based fragment screens.
AEGIS TRAINING (WP5)
Integrative training was an core aim of AEGIS. Six training schools were implemented and hosted by AEGIS partners from industry and academia. Theses focused on biophysical and biochemical assays in drug discovery (University Uppsala and Ridgeview Instruments), medicinal chemistry (University Groningen), fragment-based screening, NMR, basic interaction analysis (Helmholtz Zentrum München), drug discovery in industry, industry-academia networking, rare diseases (Novartis), computational methods in drug development (Institut Pasteur) and Structural biology, X-ray crystallography and NMR (Jagellonian University). The schools were extremely successful and productive and generated novel ideas from interactions and discussions during the meetings. Next to the regular thesis committee meetings and local training and mentoring, 27 literature webinars were organized.
Screening results for active fragments were analysed for their ability to induce new pockets and interact with transient features in the protein binding interfaces. Novel methods to validate and identify fragment binding poses using paramagnetic NMR, including the development of novel paramagnetic lanthanide binding tags, were developed and demonstrated with AEGIS targets. We implemented novel methods using NMR and molecular dynamics simulations for the detection and utilization of transient pockets with exciting promising results. Pharmacophore models used for computational screening were complemented with transient features detected by molecular dynamics. X-ray fragment screening was performed and structural biology information obtained was used to guide synthesis steps for medicinal chemistry optimization. A comparative analysis of the NMR and X-ray fragment screens, regarding type and quantity of hits was performed and highlighted interesting complementarities.
EXPERIMENTAL SCREENING AND STRUCTURAL BIOLOGY
A number of promising target proteins were selected for in-depth fragment-based lead discovery: T. cruzi PEX14, FPPS and Mycobacterium protein-tyrosine phosphatase (MptpB), UMP kinase (UMPK) and 14-3-3/p53. Feasibility studies were performed with well-established model systems. Furthermore, several virtual screening hits were characterized by NMR as binders and co-crystallized with PEX14 driving the protein in alternative crystal packing. The crystallization of FPPS, MptpB and UMPK was optimized, cryo-EM single particle structural analysis was performed for large target proteins. A fragment screening at AZ using 14-3-3/p53 and the AZ fragment library resulted in two fragment hits, which were further evolved by chemical synthesis.
MEDICINAL CHEMISTRY
A fragment library was designed based on multicomponent reaction (MCR) principles and physically realized with currently >700 fragment compounds plated. The physical fragment library is available to every member of the AEGIS consortium for screening purposes. Several hits in different projects were found. Hits generated by other screening methods were taken up and optimised by medicinal chemistry methods.
COMPUTATIONAL ANALYSIS (WP4)
Computational approaches focused on the identification and design of inhibitors with therapeutic potential. Computational analysis connects the hit and lead finding activities through virtual screening, molecular design (“scaffold hoppig”), fragment library design and reaction, generation of SAR models, investigation of novel effector mechanisms exploiting original computational methods, including molecular dynamics (MD) and transitional functional mechanism modelling. Excellent results were obtained regarding these objectives: novel inhibitors were derived for various AEGIS targets, which were validated and further developed using experimental methods. New computational methods were implemented for fast and efficient analysis of NMR-based fragment screens.
AEGIS TRAINING (WP5)
Integrative training was an core aim of AEGIS. Six training schools were implemented and hosted by AEGIS partners from industry and academia. Theses focused on biophysical and biochemical assays in drug discovery (University Uppsala and Ridgeview Instruments), medicinal chemistry (University Groningen), fragment-based screening, NMR, basic interaction analysis (Helmholtz Zentrum München), drug discovery in industry, industry-academia networking, rare diseases (Novartis), computational methods in drug development (Institut Pasteur) and Structural biology, X-ray crystallography and NMR (Jagellonian University). The schools were extremely successful and productive and generated novel ideas from interactions and discussions during the meetings. Next to the regular thesis committee meetings and local training and mentoring, 27 literature webinars were organized.
"INNOVATION
New experimental and computational methods enhanced the progress of AEGIS but are also published and thus available for the research community. The comparative evaluation of various fragment screening approaches, co-crystallisation of fragments and and molecular dynamics to detect invisible pockets reaveled unexpected interesting results, opening new ways for the inhibitor development. Together with the new fragment library based on multicomponent reactions new chemical matter was identified for the AEGIS targets and is undergoing preclinical development. Very exciting progress was made with targeting glycosome biogenesis in trypanosome, where novel leads and a novel target were identified. The development of intracellular assays using LigandTracer aided target validation. Productive secondments with other AEGIS partners - especially with the industrial partners and AEGIS training schools providing important skills and complementary training.
Thus, AEGIS has been very effective in training a new generation of intersectoral and multi-disciplinary scientists who will promote innovation of drug discovery in Europe. A final highlight was the well received international conference ""New Frontiers in Structure-Based Drug Discovery"", which was organized in cooperation with the MSCA ITN TASPPI."
New experimental and computational methods enhanced the progress of AEGIS but are also published and thus available for the research community. The comparative evaluation of various fragment screening approaches, co-crystallisation of fragments and and molecular dynamics to detect invisible pockets reaveled unexpected interesting results, opening new ways for the inhibitor development. Together with the new fragment library based on multicomponent reactions new chemical matter was identified for the AEGIS targets and is undergoing preclinical development. Very exciting progress was made with targeting glycosome biogenesis in trypanosome, where novel leads and a novel target were identified. The development of intracellular assays using LigandTracer aided target validation. Productive secondments with other AEGIS partners - especially with the industrial partners and AEGIS training schools providing important skills and complementary training.
Thus, AEGIS has been very effective in training a new generation of intersectoral and multi-disciplinary scientists who will promote innovation of drug discovery in Europe. A final highlight was the well received international conference ""New Frontiers in Structure-Based Drug Discovery"", which was organized in cooperation with the MSCA ITN TASPPI."