Design of dual ligands using excessive pharmacophore query alignment : from 7th German Conference on Chemoinformatics: 25 CIC-Workshop Goslar, Germany, 6 - 8 November 2011

Dual- or multi-target ligands have gained increased attention in the past years due to several advantages, including more simple pharmacokinetic and phamarcodynamic properties compared to a combined application of several drugs. Furthermore multi-target ligands often possess improved efficacy. We present a new approach for the discovery of dual-target ligands using aligned pharmacophore models combined with a shape-based scoring. Starting with two sets of known active compounds for each target, a number of different pharmacophore models is generated and subjected to pairwise graph-based alignment using the Kabsch-Algorithm. Since a compound may be able to bind to different targets in different conformations, the algorithm aligns pairs of pharmacophore models sharing the same features which are not necessarily at the exactly same spatial distance. Using the aligned models, a pharmacophore search on a multi-conformation-database is performed to find compounds matching both models. The potentially “dual” ligands are scored by a shape-based comparison with the known active molecules using ShaEP. Using this approach, we performed a prospective fragment-based virtual screening for dual 5-LO/sEH inhibitors. Both enzymes play an important role in the arachidonic acid cascade and are involved in inflammatory processes, pain, cardiovascular diseases and allergic reactions. Beside several new selective inhibitors we were able to find a compound inhibiting both enzymes in low micromolar concentrations. The results indicate that the idea of aligned pharmacophore models can be successfully employed for the discovery of dual-target ligands

Design of dual ligands using excessive pharmacophore query alignment

Dual- or multi-target ligands have gained increased attention in the past years due to several advantages, including more simple pharmacokinetic and phamarcodynamic properties compared to a combined application of several drugs. Furthermore multi-target ligands often possess improved efficacy. We present a new approach for the discovery of dual-target ligands using aligned pharmacophore models combined with a shape-based scoring. Starting with two sets of known active compounds for each target, a number of different pharmacophore models is generated and subjected to pairwise graph-based alignment using the Kabsch-Algorithm. Since a compound may be able to bind to different targets in different conformations, the algorithm aligns pairs of pharmacophore models sharing the same features which are not necessarily at the exactly same spatial distance. Using the aligned models, a pharmacophore search on a multi-conformation-database is performed to find compounds matching both models. The potentially “dual” ligands are scored by a shape-based comparison with the known active molecules using ShaEP. Using this approach, we performed a prospective fragment-based virtual screening for dual 5-LO/sEH inhibitors. Both enzymes play an important role in the arachidonic acid cascade and are involved in inflammatory processes, pain, cardiovascular diseases and allergic reactions. Beside several new selective inhibitors we were able to find a compound inhibiting both enzymes in low micromolar concentrations. The results indicate that the idea of aligned pharmacophore models can be successfully employed for the discovery of dual-target ligands

SAR by Space: Enriching Hit Sets from the Chemical Space

We introduce SAR by Space, a concept to drastically accelerate structure-activity relationship (SAR) elucidation by synthesizing neighboring compounds that originate from vast chemical spaces. The space navigation is accomplished within minutes on affordable standard computer hardware using a tree-based molecule descriptor and dynamic programming. Maximizing the synthetic accessibility of the results from the computer is achieved by applying a careful selection of building blocks in combination with suitably chosen reactions; a decade of in-house quality control shows that this is a crucial part in the process. The REAL Space is the largest chemical space of commercially available compounds, counting 11 billion molecules as of today. It was used to mine actives against bromodomain 4 (BRD4). Before synthesis, compounds were docked into the binding site using a scoring function, which incorporates intrinsic desolvation terms, thus avoiding time-consuming simulations. Five micromolar hits have been identified and verified within less than six weeks, including the measurement of IC50 values. We conclude that this procedure is a substantial time-saver, accelerating both ligand and structure-based approaches in hit generation and lead optimization stages

Entwicklung Orthogonaler Screening-Systeme für Metallo-β-Lactamasen und die sEH-Phosphatase

Im Rahmen dieser Dissertation wurden drei bakterielle Enzyme, die Metallo-β-Lactamasen NDM-1 (New Delhi Metallo-β-Lactamase 1), VIM-1 (Verona-Integron Encoded Metallo-β-Lactamase 1) und IMP-7 (Imipenemase 7), sowie ein humanes Enzym, die sEH-Phosphatase, behandelt. Das Auftreten multiresistenter Bakterien ist eine alarmierende Entwicklung. Dabei ist das vermehrte Erscheinen von Metallo-β-Lactamasen (MBLs) in Gramnegativen Bakterien zu beobachten, die von Inhibitoren anderer β-Lactamasen unbeeinflusst bleiben. MBLs sind Enzyme, die β-Lactam-Antibiotika hydrolysieren und somit unwirksam machen. β-Lactam-Antibiotika hemmen die Zellwandsynthese von Bakterien und haben keinen Einfluss auf menschliche Zellen. Daher sind sie für den Menschen sehr gut verträglich und werden oft eingesetzt. Gerade diese häufige Verwendung und der Fehleinsatz führen vermehrt zur Resistenzbildung. Suche nach neuen Wirkstoffen zur Behandlung von Pathogenen mit Resistenz ist von äußerster Dringlichkeit, da die Resistenzen sich in kürzester Zeit über den kompletten Planeten verbreiten. NDM-1, VIM-1 und IMP-5 wurden in E.coli überexprimiert und aufgereinigt, um die rekombinanten Enzyme zu erhalten. Damit wurde zunächst ein Fluoreszenz-Intensitäts-Assay entwickelt, um die Wirksamkeit möglicher Inhibitoren zu quantifizieren. Als Testsubstanzen wurden elf zugelassene Wirkstoffe gewählt, die eine Thiol-Gruppe enthalten, da bekannt ist, das Thiole Zink-abhängige Proteine inhibieren. Weiterhin wurden Thermal Shift Assays durchgeführt, um zwischen Liganden, die durch Bindung an die MBL inhibieren, und Liganden, die nur dadurch inhibieren, dass sie der Bindetasche das nötige Zink entziehen, unterscheiden zu können. Substanzen, die Inhibition im Assay zeigten und keine Zink-Chelatoren waren, wurden weiterhin auf Aktivität in bakteriellen Zellen untersucht. Dafür wurden pathogenene Stämme aus Patienten sowie mit den Resistenzplasmiden transfizierte Laborstämme einem Test auf Antibiotikaempfindlichkeit unterzogen. Die Wirksamkeit von Imipenem sollte in Kombination mit den Testsubstanzen wieder hergestellt werden. Insgesamt wurden vier Substanzen mit nicht-antiinfektiösen Indikationen gefunden, die MBLs im niedrig-mikromolaren Bereich inhibieren und die Wirksamkeit von Imipenem in Bakterien partiell wieder herstellen. In einem zweiten Ansatz wurden Fragmente mittels Docking ausgewählt und ebenfalls im Fluoreszenz-basierten Assay getestet. Die Bestätigung der Bindung erfolgte in diesem Fall mit STD-NMR und die Bestimmung der Dissoziationskonstante des besten Fragments mittels Messung der Chemical Shift Perturbation im NMR. In diesem Projekt wurde leider kein pan-Inhibitor für alle MBLs gefunden, allerdings ein Fragment mit hoher Bindeeffizienz zur NDM-1. Die lösliche Epoxid-Hydrolase (englisch: soluble Epoxid Hydolase, sEH) katalysiert die Umsetzung von Epoxyeicosatriensäuren (EETs), Lipidmediatoren mit entzündungshemmenden und kardiovaskulär-protektiven Eigenschaften, zu Dihydroxyeicosatriensäuren (DHETs). Diese Reaktion ist ein Bestandteil der Arachidonsäurekaskade. Das Enzym besteht aus zwei Domänen mit unterschiedlichen katalytischen Funktionen, einerseits der viel erforschten Cterminalen Epoxid-Hydrolase-Domäne, aber auch der N-terminalen Domäne, die eine Phosphatase-Eigenschaft zeigt. Die N-terminale Domäne katalysiert die Hydrolyse von Phosphat-Monoestern, Isoprenoid- sowie Lipid-Phosphaten. Die biologische Funktion dieser Domäne ist nicht aufgeklärt, und die Phosphatase Aktivität wird von typischen Phosphatase-Inhibitoren nicht beeinflusst. Daher ist es von Interesse, einen Inhibitor zu entwickeln. Zunächst wurde ein Aktivitätsassay mit einem fluorogenen Substrat entwickelt und dieser in verschiedene Formate überführt, um in unterschiedlichen Größen testen zu können. Im 96well Format wurden mögliche Inhibitoren getestet, die mittels Docking ausgesucht wurden. Allerdings wurden nur Inhibitoren mit IC50s über 100 μM gefunden oder Inhibitoren, die Sulfonsäure-Strukturen aufweisen. Im 384well Format wurde, in Kollaboration mit dem European ScreeningPort Hamburg, ein High-Throughput Screening von ca. 17000 Substanzen durchgeführt. So wurde Oxaprozin gefunden, ein Inhibitor, der strukturelle Ähnlichkeit zu bereits bekannten Inhibitoren zeigt

Back in Person: Frontiers in Medicinal Chemistry 2023

The Frontiers in Medicinal Chemistry (FiMC) is the largest international Medicinal Chemistry conference in the German speaking area and took place from April 3(rd) to 5(th) 2023 in Vienna (Austria). Fortunately, after being cancelled in 2020 and two years (2021-2022) of entirely virtual meetings, due to the COVID-19 pandemic, the FiMC could be held in a face-to-face format again. Organized by the Division of Medicinal Chemistry of the German Chemical Society (GDCh), the Division of Pharmaceutical and Medicinal Chemistry of the German Pharmaceutical Society (DPhG), together with the Division of Medicinal Chemistry of the Austrian Chemical Society (GoCH), the Austrian Pharmaceutical Society (oPhG), and a local organization committee from the University of Vienna headed by Thierry Langer, the meeting brought together 260 participants from 21 countries. The program included 38 lectures by leading scientists from industry and academia as well as early career investigators. Moreover, 102 posters were presented in two highly interactive poster sessions

Design and synthesis of dual modulators of soluble epoxide hydrolase and peroxisome proliferator-activated receptors

Metabolic syndrome is a complex condition which often requires the use of multiple medications as a treatment. The resulting problems of polypharmacy are increase in side effects, drug-drug interactions, and its high economic cost. Development of multitarget compounds is a promising strategy to avoid the complications arising from administration of multiple drugs. Modulators of peroxisome proliferator-activated receptors (PPARs) are established agents in the treatment of dyslipidaemia, hyperglycaemia, and insulin resistance. Inhibitors of soluble epoxide hydrolase (sEH) are under evaluation for their use in cardiovascular diseases. In the present study, a series of dual sEH/PPAR modulators containing a pyrrole acidic headgroup and a urea pharmacophore were designed, synthesized, and evaluated in vitro using recombinant enzyme and cell-based assays. Compounds with different activity profiles were obtained which could be used in the treatment of metabolic syndrome

Frontiers in Medicinal Chemistry 2022 Goes Virtual

The Frontiers in Medicinal Chemistry (FiMC) meeting, which represents the largest international medicinal chemistry conference in Germany, took place from March 14(th) to 16(th) 2022 in a fully virtual format. Organized by the Division of Medicinal Chemistry of the German Chemical Society (GDCh) together with the Division of Pharmaceutical & Medicinal Chemistry of the German Pharmaceutical Society (DPhG) and a "local" organization committee from the University of Freiburg headed by Manfred Jung, the meeting brought together 271 participants from around 20 countries. The program included 33 lectures by leading scientists from industry and academia as well as early career investigators. 67 posters were presented in two poster sessions and with over 20.000 poster abstract downloads. The general organization and the time-shift function were very much appreciated as demonstrated by almost 600 on-demand contents retrieved. The online format fitted perfectly to bring together medicinal chemists from academia and industry across the globe