Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientists.

This paper describes the structure-based design of a preliminary drug candidate against COVID-19 using free software and publicly available X-ray crystallographic structures. The goal of this tutorial is to disseminate skills in structure-based drug design and to allow others to unleash their own creativity to design new drugs to fight the current pandemic. The tutorial begins with the X-ray crystallographic structure of the main protease (Mpro) of the SARS coronavirus (SARS-CoV) bound to a peptide substrate and then uses the UCSF Chimera software to modify the substrate to create a cyclic peptide inhibitor within the Mpro active site. Finally, the tutorial uses the molecular docking software AutoDock Vina to show the interaction of the cyclic peptide inhibitor with both SARS-CoV Mpro and the highly homologous SARS-CoV-2 Mpro. The supporting information (supplementary material) provides an illustrated step-by-step guide for the inhibitor design, to help readers design their own drug candidates for COVID-19 and the coronaviruses that will cause future pandemics. An accompanying preprint in bioRxiv [https://doi.org/10.1101/2020.08.03.234872] describes the synthesis of the cyclic peptide and the experimental validation as an inhibitor of SARS-CoV-2 Mpro.

Templated Synthesis of End-Functionalized Graphene Nanoribbons through Living Ring-Opening Alkyne Metathesis Polymerization.

Atomically precise bottom-up synthesized graphene nanoribbons (GNRs) are promising candidates for next-generation electronic materials. The incorporation of these highly tunable semiconductors into complex device architectures requires the development of synthetic tools that provide control over the absolute length, the sequence, and the end groups of GNRs. Here, we report the living chain-growth synthesis of chevron-type GNRs (cGNRs) templated by a poly-(arylene ethynylene) precursor prepared through ring-opening alkyne metathesis polymerization (ROAMP). The strained triple bonds of a macrocyclic monomer serve both as the site of polymerization and the reaction center for an annulation reaction that laterally extends the conjugated backbone to give cGNRs with predetermined lengths and end groups. The structural control provided by a living polymer-templated synthesis of GNRs paves the way for their future integration into hierarchical assemblies, sequence-defined heterojunctions, and well-defined single-GNR transistors via block copolymer templates.