It was quite an ordeal, just in case someone runs into a similar problem.
Advice: don't try to upgrade python on a given Ubuntu distribution!!!!
* reinstall jupyter
#+begin_src
sudo dpkg --purge python3-ptyprocess
sudo -H pip3 install --upgrade --force-reinstall --no-cache-dir jupyter
sudo -H pip3 install --upgrade --force-reinstall --no-cache-dir numpy
sudo -H pip3 install --upgrade --force-reinstall --no-cache-dir pymatbridge
sudo -H pip3 install --upgrade --force-reinstall --no-cache-dir matlab_kernel
#+end_src
* check https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting
#+begin_src
python3 -m matlab_kernel.check
#+end_src
That told me to look for a matlab solution
* matlab solution for Ubuntu 16.04
https://de.mathworks.com/matlabcentral/answers/403561-import-error-matlab-engine-in-python
** solve the gcc library problem
#+begin_src
LD_LIBRARY_PATH=/usr/local/lib64/:$LD_LIBRARY_PATH
$ export LD_LIBRARY_PATH
$ sudo apt-add-repository ppa:ubuntu-toolchain-r/test
$ sudo apt-get update
$ sudo apt-get install gcc-6 g++-6
#+end_src
** install the engine again
#+begin_src
cd /usr/local/MATLAB/R2019a/extern/engines/python/
sudo /usr/bin/python3 setup.py install
#+end_src
** Start the engine
DONE!