Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig‐Maximilians‐Universität München NOVEL CHEMICAL TOOLS FOR THE MODULATION OF TWO PORE CHANNEL 2 Susanne Daniela Gerndt aus Schweinfurt 2020 Erklärung Diese Dissertation wurde im Sinne von § 7 der Promotionsordnung vom 28. November 2011 von Herrn Prof. Franz Bracher betreut. Eidesstattliche Versicherung Diese Dissertation wurde eigenständig und ohne unerlaubte Hilfe erarbeitet. München, den 29.06.2020 ____________________________ Susanne Daniela Gerndt Dissertation eingereicht am: 01.07.2020 1. Gutachter: Prof. Dr. Franz Bracher 2. Gutachter: Prof. Dr. Dr. Christian Grimm Mündliche Prüfung am 27.07.2020 Danksagung An dieser Stelle möchte ich mich ganz herzlich bei allen bedanken, die diese Arbeit durch viele große und kleine Beiträge erst ermöglicht haben: Allen voran Herrn Prof. Dr. Franz Bracher für dieses interessante und abwechslungsreiche Thema und seine stets großzügige Unterstützung und Förderung während der vergangenen Jahre. Ebenso bedanken möchte ich mich bei den Mitgliedern der Prüfungskommission, vor allem bei Prof. Dr. Dr. Christian Grimm, nicht nur für die freundliche Übernahme des Koreferats, sondern auch für die Möglichkeit mich in ein mir fachfremdes Thema einzuarbeiten und viel Neues zu lernen. Weiter möchte ich auch meinen Kooperationspartnern danken, sei es in München Frau Prof. Dr. Angelika Vollmar, in Leipzig Prof. Dr. Michael Schaefer oder anderswo. Bei den Mitarbeitern der Analytikabteilung der Chemie und Pharmazie bedanke ich mich auch recht herzlich für die zahlreichen Messungen und die Hilfe bei analytischen Fragestellungen. Einen herzlichen Dank richte ich auch an die Arbeitsgruppen Biel, Grimm und Schaefer, die mich im Rahmen gemeinsamer Kooperationen freundlich aufgenommen und unterstützt haben. Natürlich möchte ich mich auch bei allen aktuellen und ehemaligen Kollegen aus dem Arbeitskreis Bracher für die gute Zusammenarbeit, die Unterstützung und die großartige Zeit bedanken. Vielen Dank für die zahlreichen schönen Stunden mit euch, vielen Dank für die tollen Gespräche und vielen Dank für das gemeinsame Lachen in unserem Relatively Nice Network. Vielen Dank auch an die Studenten, sei es den Hiwis, den Wahlpflicht- oder Bachelorstudenten, die mich in diesem Projekt unter meiner Betreuung tatkräftig unterstützt haben und so einen wertvollen Beitrag zu dieser Arbeit geleistet haben. Herzlichsten Dank gilt auch all denen, die sich dazu bereit erklärt haben diese Arbeit Korrektur zu lesen. Bei meinen Liebsten, meinen Freunden und meiner Familie, möchte ich mich auch für die viele Geduld, Sorge, Anteilnahme, Unterstützung, Trost aber auch die Freude, Zuversicht und Liebe, die mir geschenkt wurde bedanken. Ohne euch wäre das Alles nicht möglich gewesen. Mein größter Dank gilt Tim, der immer an mich glaubt, jeden Tag. Vielen Dank! TABLE OF CONTENTS Table of contents 1 Introduction 1 1.1 Two pore channels 1 1.2 Two pore channels and disease 2 1.2.1 Two pore channels and cancer 3 1.2.2 Two pore channels and viral infections 3 1.3 Modulators of two pore channels 4 1.4 Tetrandrine (1) – opportunities and limitations 7 2 Objectives 9 3 Results and discussion 11 3.1 Identification of novel TPC2 activators 11 3.2 Synthesis of TPC2-A1-N (16) and analogs 14 3.3 Synthesis of TPC2-A1-P (17) and analogs 22 3.4 Pharmacological investigation of TPC2 agonists 31 3.4.1 Confirmation of TPC2-A1-N (16) and TPC2-A1-P (17) as TPC2 agonists 31 3.4.2 Structure-activity relationships for TPC2-A1-N (16) and analogs 33 3.4.3 Structure-activity relationships for TPC2-A1-P (17) and analogs 39 3.4.4 Further results of the novel TPC2 agonists 44 3.4.5 Malleable cation selectivity of TPC2 46 3.4.6 The race to identify new TPC activators 48 3.5 A new generation of TPC2 inhibitors 51 3.5.1 Collection of alkaloids and 1-benzylisoquinolines 51 3.5.2 Synthesis plan 53 3.5.3 Synthesis of a new generation of TPC2 inhibitors 58 3.6 Pharmacological investigation of TPC2 antagonists 71 3.6.1 First identification of the truncated TPC2 inhibitors 71 3.6.2 Analysis of the compound library 74 3.6.3 TPC2 and cancer 78 3.6.4 Separation of the enantiomers 82 3.6.5 Expanding the TPC2 inhibitor panel 83 3.7 Side Projects 85 3.7.1 The isoquinoline-benzylisoquinoline alkaloid rac-muraricine (213) 85 3.7.2 The TRPML inhibitors ML-SI1 (214) and ML-SI3 (215) 86 I TABLE OF CONTENTS 4 Summary 88 5 Experimental part 95 5.1 Preparation of TPC2 activators 97 5.1.1 General procedures 97 5.1.2 Synthetic procedures 98 5.1.2.1 Synthesis of TPC2-A1-N (16) and analogs 98 5.1.2.2 Synthesis of TPC2-A1-P (17) and analogs 148 5.2 Preparation of TPC2 inhibitors 168 5.2.1 General procedures 168 5.2.2 Synthetic procedures 170 5.2.2.1 Synthesis of arylethylamine building blocks 170 5.2.2.2 Synthesis of enol ethers 176 5.2.2.3 N-Acyl Pictet-Spengler reaction 179 5.2.2.4 Lithium alanate reductions of carbamates and deprotections of carbonates 183 5.2.2.5 Chan-Evans-Lam couplings 190 5.2.2.6 Further reactions 201 5.2.2.7 Substances received from other sources 204 5.3 Biological methods 208 5.3.1 High throughput screening (HTS) 208 5.3.2 Single cell calcium imaging 208 5.3.3 MTT 209 5.3.4 Agar diffusion test 210 6 Appendices 211 6.1 Abbreviations 211 6.2 References 214 II INTRODUCTION 1 Introduction “The most fruitful basis of the discovery of a new drug is to start with an old drug.” Sir James Black With these words the pharmacologist and Nobel laureate Sir James Black established a basis for drug repurposing. The fact that an already known drug is used for a new indication that differs from the original indication is called drug repurposing. Thereby new targets can be identified for the old drugs. Another approach, beside these new targets, is that the scaffolds of the old drugs or natural compounds can also serve as an inspiration for the synthesis of novel small-molecules[1]. This thesis deals with two pore channel 2 (TPC2) as the target and tetrandrine (1, Figure 1) as the natural compound with the need to be developed. In 2015, Sakurai et al. linked the entry of Ebola virus into host cells to two pore channels (TPCs). The inhibition of TPCs with tetrandrine (1) halted virus trafficking and prevented infection[2], creating the fundament for this work. Figure 1: Chemical structure of the alkaloid tetrandrine (1), identified as a TPC2 inhibitor. 1.1 Two pore channels Two pore channels are part of the family of voltage-gated ion channels and are localized in the endo-lysosomal system. They share parts of the sequential identity with voltage-gated calcium [3] (Cav) and sodium (Nav) channels . Two isoforms of two pore channels (TPC1 and TPC2) can be found in primates. TPC1 is preferentially found in early endosomal compartments and TPC2 in late endosomal and lysosomal compartments[4-6]. In 2016, Kintzler and Stroud presented the crystal structure of the NAADP antagonist trans-Ned-19 (2) bound to TPC1 from Arabidopsis 1 INTRODUCTION thaliana[7]. The cryo-EM structure of human TPC2 has recently been resolved by She et al.[8] and verifies the dimeric nature and the duplicated domains of two pore channels. Two times six transmembrane helices form one domain and two domains form the ion channel. TPCs are non-selective cation channels, permeable to calcium and sodium and they are involved in endo-lysosomal trafficking, autophagy, mTOR and TFEB signaling[9]. Whether TPC2 is sodium or calcium permeable was subject of controversial debates in the last decade. While TPC2 was first described as non-selective, calcium permeable cation channel activated by NAADP (3)[10-14], other research groups claimed that TPC2 was a sodium-selective channel activated [15, 16] by the endo-lysosomal phosphoinositide PI(3,5)P2 (4) . Both views independently received support in the past couple of years[5, 17-21] and the controversy has just recently been resolved[22] in the course of this project, as described in chapter 3.4.5. Two pore channels have been a hot topic in recent literature, not only because of their controversially discussed ion permeability but also because of their involvement in various diseases like viral and bacterial infections and cancer cell migration. This makes two pore channels a promising target for drug research. 1.2 Two pore channels and disease As mentioned before, in recent years TPCs have emerged as highly exciting potential drug targets for a number of diseases associated with the endo-lysosomal system[23]. Dysfunction of TPCs has been found to interfere with cholesterol trafficking resulting in fatty liver disease[5], the β-adrenergic stimulation of glucagon secretion in diabetes[24] and β-adrenoceptor signaling in the heart in cardiovascular diseases[25]. Melanin production and pigmentation are also influenced by TPC activity[26-28]. Furthermore, Parkinson’s disease caused by LRRK2 mutations has been linked to TPC functions[29]. In addition, several bacterial toxins such as diphtheria toxin, anthrax toxin, cholera toxin, or Pasteurella multocida toxin have been shown to require functional TPCs[4, 6]. Beside its role in bacterial infections, TPCs have been demonstrated to play a role in various infectious diseases such as Ebola filovirus, Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or HIV-1 retrovirus infections [2, 30-33]. Furthermore there is a growing amount of evidence that TPCs are necessary for sustaining cancer hallmarks like cell migration and neoangiogenesis[9, 34-36].