Metal-dependent catalysis of nanozymes: First steps towards computational nanoenzymology

Project Information

CompNanozymes

Grant agreement ID: 843117

DOI

10.3030/843117

Project closed

EC signature date 12 April 2019

Start date 1 June 2019

End date 31 May 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 183 473,28

EU contribution

€ 183 473,28

Coordinated by

FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA
Italy

Periodic Reporting for period 1 - CompNanozymes (Metal-dependent catalysis of nanozymes: First steps towards computational nanoenzymology)

Reporting period: 2019-06-01 to 2021-05-31

Summary of the context and overall objectives of the project

Summary:

Monolayer-protected gold nanoparticles (MPGNs) can be functionalized to produce nanodevices with unique properties. These have led to a wide range of applications in fields including pollutant removal, chemosensing, cancer diagnostics and therapy, and even catalysis. The molecules forming the outer coating monolayer are the main contributor to the nanoparticle’s functionality, however, its fundamental behavior at the level of the outer coating monolayer remains poorly understood, limiting our ability to rationally design functionalized MPGNs. We focused on MPGN-based artificial enzymes - so called nanozymes - that are a novel, highly promising, and yet poorly understood nanoparticle-based technology with potentially revolutionary applications for human health (e.g. gene therapy) and technology. Particularly, we studied a new class of nanozymes with promising ribonuclease-like activity., in which the nanocatalysis is facilitated by metal ion(s) chelated by the coating molecules of MPGNs. We used simulations flanked by experimental methods including nuclear magnetic resonance (NMR) and kinetic measurements, to dissect how MPGN-based nanozymes operate at the atomic level.


Objectives:

Objective 1. To understand the structure and dynamics of the nanozyme/substrate interface.
We studied 2 structurally similar gold nanoparticles that cleave an RNA model system with different efficiency. Using our closed-loop approach, we revealed differently preorganized coating monolayers of these nanosystems allowing a different nature of substrate recognition. We showed that more efficient nanozyme mimics two-metal-ion enzymes for nucleic acid processing.

Objective 2. To understand nanozyme reactivity in order to increase the catalytic efficiency of monolayer protected gold nanoparticles.
Here, we focused on a new generation of DNA cleaving nanozymes. Having solved the ex-novo parametrization and MD setup, we run a series of classical MD simulations to detect and characterize the formation of Michaelis-Menten complexes at the nanozyme/substrate interface. Our simulations returned two possible prereactive states and we thus clarified the single metal ion mechanism of this new class of nanonucleases.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Results:

The project successfully applied molecular simulations to nanozymes, coupled closely with NMR experiments, and has revealed how MPGNs carry out the metal-aided hydrolysis of RNA and DNA substrates. We have developed a transferable closed-loop protocol for studying structure-function relationship of functionalized nanoparticles. The project generated unprecedented knowledge on nanozyme catalysis and filled the knowledge gap in the understanding of nanoparticle structure-function relationships. The knowledge from our studies can be used for a rational design of more efficient nanozymes cleaving nucleic acids. Ultimately, the project has offered the possibility of controlling phosphoryl transfer reactions (e.g. for DNA-based technologies) in complex environments.

Exploitation and Dissemination:

- peer-reviewed journal articles:

1) Pecina, A.; Rosa-Gastaldo, D.; Riccardi, L.; Franco-Ulloa, S.; Milan, E.; Scrimin, P.; Mancin, F.; De Vivo, M.: On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes, ACS Catalysis 2021, 11, 8736. Front Cover.

2) Czescik, J.; Zamolo, S.; Darbre, T.; Rigo, R.; Sissi, C.; Pecina, A; Riccardi, L.; De Vivo, M.; Mancin, F.; Scrimin, P.: A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex; Angewandte Chemie Int. 2021, 133, 1443.

- conference paper:

1) Pecina, A.; Scrimin, P.; Mancin, F.; De Vivo, M.: Mechanistic Insight into the Phosphodiester Bond Hydrolysis of Nanozymes; 2021, DOI: 10.11159/tann21.115


- conferences:


1) May 2021 - Talk; TANN21: 5th International Conference of Theoretical and Applied Nanoscience and Nanotechnology, Niagara Falls, Canada (Virtually due to Covid-19 pandemics), DOI: 10.11159/tann21.11

2) Apr 2021- Talk; ACS Spring National Meeting and Expo: Macromolecular Chemistry – The Second Century, Virtually due to Covid-19 pandemics

3) March 2021 - Poster and Flash Talk; VIZBI 2021: 11th international meeting on Visualizing Biological Data, EMBL (Virtually due to Covid-19 pandemics)

4) Nov 2020 - Invited Plenary Lecture; SeedMol: 8th Symposium on Electronic Structure and Molecular Dynamics, Brasìlia, DF, Brasil (Virtually due to Covid-19 pandemics)

5) Mar 2020 - Talk; ACS Spring National Meeting and Expo: Macromolecular Chemistry: The Second Century, Philadelphia, USA; (presented virtually as a poster on SciMeetings platform due to Covid-19 pandemics)

6) Oct 2019 - Talk; NANOCON 2019: 11th International conference on nanomaterials – research & applications, Brno, Czech Republic

7) Jun 2019 - Talk and Poster; BioExcel Summer School on Biomolecular Simulations, Sardinia, Italy


- Organizing

1) May 2021 – CECAM-flagship workshop on Rational design of functionalized nanoparticles: Theory meets Experiments 2021, Genoa, Italy. Due to Covid-19 postponed to 2022; (https://www.cecam.org/workshop-details/1049)

2) May 2019 – CECAM-node workshop on Challenges in modeling and simulations of nanoparticles in complex environments, Genoa, Italy; (https://www.cecam.org/workshop-details/74)



- Dissemination, Communication and Outreach activities

1) Jun 2021 - Lecture; Applicants´ On-line Workshop on MSCA Postdoctoral Fellowships (The National Information Centre for European Research, Czech Republic)

2) Oct 2020 - Lecture; PhD course FRESHERS: training on skills for research career (Masaryk University in Brno, Czech Republic)

3) Dec 2019 - Mentoring; Czexpats in Science Workshop “Na postdoc ven” (CIIRS, Czech Republic)

4) Dec 2019 - Popular science article; IIT OPENTALK online journal, Genoa, Italy.

5) multiple social media, e.g. Twitter (@madAniceP, @devivo_marco, @IITalk, @fabrizio_mancin), Facebook, LinkedIn, ResearchGate, YouTube channel etc.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

State of the Art and Results:

The project generated unprecedented knowledge on nanozyme catalysis. The outcomes of the project showed the way how to finely regulate catalytic efficiency of nucleic-acid cleaving nanozymes. Our mechanistic insights also reinforced the parallelism of such nanozymes with proteins, advocating for the rational design of nanonucleases with enhanced efficiency. Ultimately, the project thus partially filled the significant knowledge gap in our understanding of nanoparticle structure-function relationships and set new standards in the nascent field of computational nanodesign.

Socio-Economic Impact:

The project has in principle impacted the field of nanochemistry by offering the possibility of controlling phosphoryl transfer reactions (e.g. for DNA-based technologies) in complex environments. Moreover, functionalized nanoparticles for recognition and catalysis are crucial for drug delivery, detoxification, and smart materials. Understanding nanoparticle-environment interactions is also fundamental when developing nanoparticle applications for nanomedicine (consider, for example, the protein corona that controls a nanoparticle’s biological behavior), quantum electronics, nonlinear optics, photonics, and composite materials. The outcomes of the project thus have a direct and positive socioeconomic impact on areas such as energy and healthcare.

RNA-model system cleaving Nanozymes

Functionalized gold nanozyme binding HPNP substrate, depicted with its surface as well as ligands

Two precatalytic complexes of DNA cleaving gold nanozyme (revealed by MD simulations)

DNA cleaving gold nanozyme