**4. Conclusions**

We proposed a compartmental model for the hippocampal synapse CA3-CA1. Our goal was to provide a simple and portable, python-based program to run kinetics simulations of the synaptic transmission, which embodied both pre- and post-synaptic activity. The rationale that drove us through the implementation, as well as the application, of this model was to focus on the integration between system biology and structural biology viewpoints. Exploiting this hybrid multiscale approach, we analyzed the impact that single disease associated variants of NMDA receptors, related to neurological disorders and cognitive impairments, may have on the whole synaptic transmission process. We were able to consistently reproduce experimental data and to quantitatively infer molecular-level causality of a variant-related functional impairment. Therefore, these results show the predictive power of such a multiscale approach, aimed at observing behavioral shifts of a complex system that emerge from amplification of small, quantifiable, molecular-level alterations.

A future improvement of our model will allow us to explicitly quantify synaptic plasticity events by adding further biological details, e.g., AMPA receptors conductance modulation and translocation by CaMKII-mediated phosphorylation. The next step will be to extend the structural analysis to the multiple molecular entities involved in the transmission and modulation processes, recalibrating the kinetic constants of the interactions according to the conformational rearrangements caused by specific mutations. This will allow us to explicitly simulate the molecular effects, as well as the impact on the single-neuron functionality, of mutational signatures linked to neurological and cognitive impairments, which affect one or multiple entities of the modeled interactome. Finally, this approach may be extended to post-synaptic receptors belonging to other families, such as G-protein coupled receptors.

**Supplementary Materials:** Supplementary Materials can be found at https://www.mdpi.com/14 22-0067/22/4/1536/s1, Figure S1: AMPA-mediated EPSPs generated by pre-synaptic stimulations composed of a single glutamate pulse or a burst of 5 glutamate pulses delivered at 100 Hz, Figure S2: Kinetic schemes used for simulating the gating mechanisms of NMDA and AMPA receptors, Table S1: Comparison between peak open probability and deactivation time constants values obtained from our implementation and the ones reported by the original models, Table S2: List of the parameters used in the equations of the CPC module.

**Author Contributions:** Conceptualization, P.M., R.R., and A.G.; methodology, P.M.; software, P.M.; validation, P.M. and R.R.; formal analysis, P.M.; investigation, P.M. and R.R.; resources, A.G.; data curation, P.M. and R.R.; writing—original draft preparation, P.M. and R.R.; writing—review and editing, P.M., R.R., and A.G.; supervision, R.R. and A.G.; project administration, R.R. and A.G.; funding acquisition, A.G. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the ordinary research fund form the Dept. of Biotechnology of the University of Verona.

**Data Availability Statement:** All the code used for implementing and simulating the compartmentalized model is stored in a publicly available github repository (https://github.com/pietromicheli/ CA3-CA1\_SynapticModel) where a jupyter notebook file for running simulations and performing basic analysis can be also found.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
