Computational optimization of angiotensin-converting enzyme 2 for SARS-CoV-2 Spike molecular recognition

• Main Authors: Lorenzo Di Rienzo, Michele Monti, Edoardo Milanetti, Mattia Miotto, Alberto Boffi, Gian Gaetano Tartaglia, Giancarlo Ruocco
• Format: Article
• Language: English
• Published: Elsevier 2021-01-01
• Series: Computational and Structural Biotechnology Journal
• Subjects: Molecular design; SARS-CoV-2; ACE2-Spike interaction; Molecular recognition
• Online Access: http://www.sciencedirect.com/science/article/pii/S2001037021001975

Since the beginning of the Covid19 pandemic, many efforts have been devoted to identifying approaches to neutralize SARS-CoV-2 replication within the host cell. A promising strategy to block the infection consists of using a mutant of the human receptor angiotensin-converting enzyme 2 (ACE2) as a decoy to compete with endogenous ACE2 for the binding to the SARS-CoV-2 Spike protein, which decreases the ability of the virus to enter the host cell. Here, using a computational framework based on the 2D Zernike formalism we investigate details of the molecular binding and evaluate the changes in ACE2-Spike binding compatibility upon mutations occurring in the ACE2 side of the molecular interface. We demonstrate the efficacy of our method by comparing our results with experimental binding affinities changes upon ACE2 mutations, separating ones that increase or decrease binding affinity with an Area Under the ROC curve ranging from 0.66 to 0.93, depending on the magnitude of the effects analyzed. Importantly, the iteration of our approach leads to the identification of a set of ACE2 mutants characterized by an increased shape complementarity with Spike. We investigated the physico-chemical properties of these ACE2 mutants and propose them as bona fide candidates for Spike recognition.