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Dependent Modeling Approach Derived from Semi-Empirical Quantum Mechanical Calculations

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Dependent Modeling Approach Derived from Semi-Empirical Quantum Mechanical Calculations 3D-QSAR/QSPR Based Surface- Dependent Modeling Approach Derived From Semi-Empirical Quantum Mechanical Calculations 3D-QSAR/QSPR-basierter, oberflächenabhängiger Modellierungsansatz, abgeleitet von semi-empirischen quantenmechanischen Rechnungen Der Naturwissenschaftlichen Fakultät der Friedrich-Alexander-Universität Erlangen-Nürnberg Zur Erlangung des Doktorgrades Dr. rer. nat. vorgelegt von Marcel Youmbi Foka aus Kamerun Als Dissertation genehmigt von der Naturwissenschaftlichen Fakultät/ vom Fachbereich Chemie und Pharmazie der Friedrich-Alexander-Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 05.12.2018 Vorsitzender des Promotionsorgans: Prof. Dr. Georg Kreimer Gutachter/in: Prof. Dr. Tim Clark Prof. Dr. Birgit Strodel Dedication In memory of my late Mother Lucienne Metiegam, who the Lord has taken unto himself on May 3, 2009. My mother, light of my life, God rest her soul, had a special respect for my studies. She had always encouraged me to move forward. I sincerely regret the fact that today she cannot witness the culmination of this work. Maman, que la Terre de nos Ancêtres te soit légère! This is a special reward for Mr. Joseph Tchokoanssi Ngouanbe, who always supported me financially and morally. That he find here the expression of my deep gratitude. i ii Acknowledgements I would like to pay tribute to all those who have made any contribution, whether scientific or not, to help carry out this work. All my thanks go especially to Prof. Dr. Tim Clark, who gave me the opportunity and means to work in his research team. I am grateful to have had him not only supervise my work but also for his patience and for giving me the opportunity to explore this fascinating topic. As it was not in my area of expertise, I really enjoyed acquiring skills in this research area. I address my sincere thanks to Dr. Nico Van Eikema Hommes, for his technical assistance. I thank Dr. Christian Cramer for introducing me to the Val-Mlr and MOE programs, for the help he has always given me, and for becoming a close friend. I thank Dr. Jr-Hung Lin for helping me to attain knowledge in VAMP, ParaSurf and Material’s Studio programs. Due to the fact that I come from a French-speaking country, my level of English is not high. For this purpose, the contribution of Dr. Victoria Jackiw from the Language Centre of the University of Erlangen-Nuremberg for correcting the English quality of my thesis was a very great contribution. I am very grateful to her for this help. I sincerely thank Mr. Justin Choapoueng Nkue and Mrs. Elise Tchokoanssi Ngouanbe for the brotherly love they have always given me. While praying for the repose of the souls of Mom Pauline Sikompe, Julienne Tagny, Jean Lonkep, Mom Lydie Teukam, and Alice Nana, allow me to extend my thanks to Mom Anne Kouatchie, Mom Elisabeth Kamgho, Bernadette Mafodjo, Martin Kugoua, Gildas Nkue, Willy Nkue, Anick, Carine, Larissa, Boris, and Cynthia Tchokoanssi, Gisele and Beatrice Youmbi, Paulette, Muriel, Lynn, Nancy, Cindy, and Erwin Choapoueng, Patricia Ngangoua, Family Ngongang, Family Wember, Family Bagnessi, Armelle Nanguep, Fabien Touko, Emmanuel Tchokoanssi, Therese Yommo, Susanne Kamdem, Odette and Paul Bati, Hugues Lengue, Armand Lonkep, Dieudonne Fogaing, Hubert Djapou, Luther Tagny, and Astride Nguetchuessi for the solidarity and for the family love they never withheld from me. Father Rigoberg Beck was kind enough to help me spiritually and emotionally during this time dedicated to my Ph.D, especially during the illness of my mother and after her death. I will not forget to thank Lißet Prechtel (R.I.P), Family Labbat-Metiogno, Dr. Eva and Radim Beranek, Family Guiffo, Brigitte Wohleben, Ferdinand Kuete, Angelika and Siegfried Balleis, Birgitt Aßmus, Alexandra Wunderlich, all the members of Christlich-Soziale Union (CSU), Odon Fokou, Dr. Pierrette Fofana, Guy Toko, Sylviane Tassing, Maila Dengel, Family Wete, Family Kuate, Family Yaneu, Family Sadjue, Family Tsumbu, Merlin Nkodja, Yanick Modjo, Gervais Gamgmeni, Emerent Prowo, Nathalie Tchamdjou, Sorelle Nsogning, everyone from Hering & Schneider GmbH, Carole Nya, Rosine Niaba, Chanceline Kamdem, Noelia Santos, Rose Kouatchet, Claude Heuyam, and Helene Kankeu for their sincere friendship, which has always united us, their sympathy and their solidarity. iii It comes from the heart to thank Simone Rennoch, Käthe and Josef Rennoch, and all the German community of Pommer for the love, affection and support they always gave me. It is a real pleasure for me to thank all the people of Computer-Chemie-Centrum in Erlangen (CCC) with whom I enjoyed working during these years of my thesis, particularly Prof. Dr. Paul von Rague Schleyer (R.I.P), Prof. Dr. Bernd Meyer, Prof. Dr. Dirk Zahn, Dr. Harald Lanig, Dr. Pawel Rodziewicz, Dr. Mateuz Wielopolski, Dr. Hakan Kayi, Dr. Ute Seidel, Dr. Jakub Goclon, Dr. Adria Gil Mestres, Dr. Ahmed Elkerdawy, Maximilian Kriebel, Dr. Pavlo Dral, Jürgen Wittman, Dr. Alexander Urban, Dr. Sebastian Schenker, Matthias Wildauer, Dr. Patrick Duchstein, Dr. Theodor Milek, Dr. Frank Beierlein, Tilo Sauertig, Oscar Roja, Heike Thomas, Dr. Christian Wick, Philipp Altmann, Bahanur Becit, Stefano Sansotta, Johannes Träg, Isabelle Schraufstetter, Nadine Scharrer, and not forgetting all the others. Finally, I would like to thank the German Academic Exchange Service (DAAD), which through its program "DAAD-STIBET Doktorandenabschlussförderung" granted me a scholarship at the end of my studies. iv Zusammenfassung In dieser Arbeit werden einige neue QSAR/QSPR Modelle für die Vorhersage physikalisch-chemischer und biologischer Aktivitäten von organischen Verbindungen beschrieben. Neue Modelle für die Berechnung der freien Solvatisierungsenergie in Wasser, Octanol und Chloroform wurden entwickelt, basierend auf Gasphase-Geometrien, die mittels AM1, AM1*, MNDO/d, und PM3-Optimierung durch VAMP berechnet wurden. Die neuen Modelle wurden durch eine Kombination der reinen Coulomb-Solvatisierungsenergie erhalten, abgeleitet aus einer SCRF-Berechnung, in Kombination mit einem Oberflächen- Integral als Funktion lokaler quantenmechanischer Eigenschaften auf der Oberfläche. Obwohl AM1* und MNDO/d keine lokale Polarisierbarkeit besitzen, wurde die Berechnung der Lösungsmitteleffekte für diese Hamiltonians durch eine Erweiterung der SCRF-routine auf s- und p-Orbitale, zu d-Orbitale ermöglicht. Die lokalen Eigenschaften wurden mit ParaSurf berechnet, basierend entweder auf der Isodichte-Oberfläche oder der sphärischen harmonischen Oberfläche. Die Modelle mit den statistisch besten Ergebnissen wurden mit der Isodichte-Oberfläche berechnet. Unter den Hamiltonians ergab AM1 die besten Vorhersagen mit (R2 = 0,92, MUE = 0,67, RMSD = 0,87), (R2 = 0,92, MUE = 0,57, RMSD = 0,73), (R2 = 0,91, MUE = 0,46, RMSD = 0,61), für die Solvatisierungsenergie in Wasser, Octanol und Chloroform. Für diese Solvatisierungsmodelle wurde herausgefunden, dass der Beitrag der jeweiligen lokalen Eigenschaft mehr als 30% für das molekulare elektrostatische Potential, (MEP, V), zwischen 15% und 25% für die lokale Ionisierungsenergie, (IEL), zwischen 15% und 20% für die lokale Elektronenaffinität, (EAL) und zwischen 10% und 18% für die lokale Polarisierbarkeit, (ĮL, POL) und die Härte, (ȘL, HARD) beträgt. Diese kleine Anzahl an verwendeten Variablen half dabei das Risiko der Erzeugung von übertrainierten Modellen erheblich zu verringern. Das Fehlen der lokalen Polarisierbarkeit für AM1* und MNDO/d äußerte sich signifikant, vor allem für die freie Solvatisierungsenergie in Wasser für neutrale und ionische Verbindungen mit einem RMSD-Unterschied von 6%, verglichen mit AM1 und PM3. Die Solvatisierungsmodelle in Wasser und Octanol, die mit neutralen Verbindungen entwickelt wurden, wurden zur Vorhersage des Octanol/Wasser-Verteilungskoeffizienten, logPow für kleine Moleküle angewandt. Für diese Verbindungen wiesen die Modelle eine sehr gute Vorhersagekraft auf, scheinen aber nur sehr eingeschränkt in der Lage zu sein, den logPow für große Moleküle zu berechnen. Der Chloroform/Wasser-Verteilungskoeffizient, logPcw für eine Reihe von kleinen Verbindungen wurde ebenfalls berechnet, um die Modelle zu validieren, wobei sehr gute statistische Ergebnisse erzielt wurden. Es wurde ein neuer mathematischer Ansatz, basierend auf klassifizierten Oberflächenabschnitten des molekularen elektrostatischen Potentials, (MEP), der lokale Ionisierungsenergie, (IEL), der lokale Elektronenaffinität, (EAL), der lokale Polarisierbarkeit, (ĮL), der Härte, (ȘL), der Elektronegativität, (ȤL, ENEG) und dem Feld senkrecht zur Oberfläche, (FN) und ihrer Kreuz-Produkte entwickelt. Dieser Ansatz unterscheidet sich grundsätzlich vom vorhergehenden polynomischen surface-integral model (SIM), dessen v Prinzip es ist, über eine molekulare Oberfläche MEP, IEL, EAL, ĮL und ȘL zu integrieren. Der neue Oberflächen-Integral-Modell-Ansatz wurde dann verwendet, um logPow Modelle für einen sehr großen Datensatz, die LOGKOW Datenbank, bestehend aus hauptsächlich neutralen, kleinen und großen Molekülen, zu erstellen. Ausgehend von den Gasphasengeometrien, die mittels AM1, AM1*, PM3, MNDO, MNDO/d und PM6 Optimierung durch VAMP erhalten wurden, wurden Modelle unter Verwendung der Isodichte-Oberfläche, beziehungsweise der vom Lösungsmittel ausgeschlossenen Oberfläche zur Berechnung der Deskriptoren, erzeugt. Es wurde herausgefunden, dass diese Modelle stark von der Flexibilität und Steifheit der Verbindungen beeinflusst werden und Verbindungen mit einer kleineren Anzahl an rotierbaren Bindungen besser vorhergesagt wurden.
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