Combining High‐Throughput Synthesis and High‐Throughput Protein Crystallography for Accelerated Hit Identification

Abstract

Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However,recent progress in PX could allowfor amore integrated role into early drug discovery.H ere,w ed emonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe ap ractical multicomponent reaction approach to acrylamides and -esters from diverse building blocks suitable for mmol scale synthesis on 96-well format and on ah igh-throughput nanoscale format in ah ighly automated fashion. High-throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID-19 causing agent, SARS-CoV-2. Our results demonstrate,t hat the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.

Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains

“…N,N-Dimethylformamide (DMF) was purchased from Sigma Aldrich (CAS No. 68-12-2, Poznań, Poland), Lanes 1kb-ladder, and Quick Extend DNA ladder (New England Biolabs, Ipswich, MA, USA), with MIC and MBC tests as described in detail in the previous work [ 16 , 17 , 18 , 19 , 20 , 21 , 22 ] and analyzed by the Tukey test indicated by ( p < 0.05): * p < 0.05, ** p < 0.1, *** p < 0.01.…”

“…Due to antimicrobial resistance, there is a need to find new potent antimicrobial drugs. There are very few reports on the antimicrobial activities of DKPs against E. coli [ 19 ]. The goal of the presented studies is to design a method for the synthesis of DKPs and to substantiate their antimicrobial potential against model E. coli strains.…”

‘Chemistry at the speed of sound’: automated 1536-well nanoscale synthesis of 16 scaffolds in parallel

“…In acoustic droplet ejection (ADE), precise nanodroplets are formed by applying acoustic waves to the stock solutions of the building blocks in the source plate and transported above to the inverted destination plate, where the reaction is taking place. 19 A total of 336 building blocks and reagents were used here, including cyclic 5-and 6-membered aromatic amidines (36), aldehydes (52) and ketones (15), isocyanides (64), carboxylic acids (71), 78 amines (46 primary and 32 secondary amines), all fitting into one 384-well source plate (Fig. 2, ESI, section 2.3 †).…”

“…Recently, the integration of HT synthesis and HT protein crystallography has emerged as a promising novel approach to shorten the ubiquitous ‘design–make–test–analyze’ cycle (DMTA). 15 …”

De novo selected hACE2 mimics that integrate hotspot peptides with aptameric scaffolds for binding tolerance of SARS-CoV-2 variants

“…As exemplified by the hACE2-mimicking hybrid ligands, many different receptor mimics could be readily created through our iterative HOLD process when we systematically combine the rational choice of hotspot peptide motif with the in vitro selection of aptameric scaffolds. Recently, protein crystallography is rapidly progressing because of the advance of high-throughput crystallization screening and spectroscopic observation by cryo-EM, thereby allowing newly emerging viruses to be structurally analyzed for hotspot identification just within a month ( 52 , 53 ). Moreover, by simply correlating the genotype with the phenotype, nucleic acid–based evolutionary techniques are continuously accelerated to discover a variety of functional oligonucleotides, including aptamers ( 54 ) and nucleozymes ( 55 ), in high throughput; by automatic screening ( 56 ), machine learning–guided selection ( 57 ), and multiparallel characterization ( 58 ), the in vitro evolution of nucleic acids has been substantially boosted to be completed even in a week ( 57 ).…”