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Dive into the research topics where Mark D. Simon is active.

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Featured researches published by Mark D. Simon.


ChemBioChem | 2014

Rapid Flow‐Based Peptide Synthesis

Mark D. Simon; Patrick L. Heider; Andrea Adamo; Alexander A. Vinogradov; Surin K. Mong; Xiyuan Li; Tatiana Berger; Rocco L. Policarpo; Chi Zhang; Yekui Zou; Xiaoli Liao; Alexander M. Spokoyny; Klavs F. Jensen; Bradley L. Pentelute

A flow‐based solid‐phase peptide synthesis methodology that enables the incorporation of an amino acid residue every 1.8 min under automatic control or every 3 min under manual control is described. This is accomplished by passing a stream of reagent through a heat exchanger into a low volume, low backpressure reaction vessel, and through a UV detector. These features enable continuous delivery of heated solvents and reagents to the solid support at high flow rate, thereby maintaining maximal concentration of reagents in the reaction vessel, quickly exchanging reagents, and eliminating the need to rapidly heat reagents after they have been added to the vessel. The UV detector enables continuous monitoring of the process. To demonstrate the broad applicability and reliability of this method, it was employed in the total synthesis of a small protein, as well as dozens of peptides. The quality of the material obtained with this method is comparable to that for traditional batch methods, and, in all cases, the desired material was readily purifiable by RP‐HPLC. The application of this method to the synthesis of the 113‐residue Bacillus amyloliquefaciens RNase and the 130‐residue DARPin pE59 is described in the accompanying manuscript.


Nature Chemical Biology | 2017

A fully automated flow-based approach for accelerated peptide synthesis

Alexander James Mijalis; Dale Arlington Thomas Iii; Mark D. Simon; Andrea Adamo; Ryan Beaumont; Klavs F. Jensen; Bradley L. Pentelute

Here we report a fully automated, flow-based approach to solid-phase polypeptide synthesis, with amide bond formation in 7 seconds and total synthesis times of 40 seconds per amino acid residue. Crude peptide purities and isolated yields were comparable to those for standard-batch solid-phase peptide synthesis. At full capacity, this approach can yield tens of thousands of individual 30-mer peptides per year.


Angewandte Chemie | 2014

Flow‐Based Enzymatic Ligation by Sortase A

Rocco L. Policarpo; Hansol Kang; Xiaoli Liao; Amy E. Rabideau; Mark D. Simon; Bradley L. Pentelute

Sortase-mediated ligation (sortagging) is a versatile, powerful strategy for protein modification. Because the sortase reaction reaches equilibrium, a large excess of polyglycine nucleophile is often employed to drive the reaction forward and suppress sortase-mediated side reactions. A flow-based sortagging platform employing immobilized sortase A within a microreactor was developed that permits efficient sortagging at low nucleophile concentrations. The platform was tested with several reaction partners and used to generate a protein bioconjugate inaccessible by solution-phase batch sortagging.


ChemBioChem | 2014

Rapid total synthesis of DARPin pE59 and barnase.

Surin K. Mong; Alexander A. Vinogradov; Mark D. Simon; Bradley L. Pentelute

We report the convergent total synthesis of two proteins: DARPin pE59 and Bacillus amyloliquefaciens RNase (Barnase). Leveraging our recently developed fast‐flow peptide‐synthesis platform, we rapidly explored numerous conditions for the assembly of long polypeptides, and were able to mitigate common side reactions, including deletion and aspartimide products. We report general strategies for improving the synthetic quality of difficult peptide sequences with our system. High‐quality protein fragments produced under optimal synthetic conditions were subjected to convergent native chemical ligation, which afforded native full‐length proteins after a final desulfurization step. Both DARPin and Barnase were folded and found to be as active as their recombinant analogues.


Organic Letters | 2016

C-Terminal Modification of Fully Unprotected Peptide Hydrazides via in Situ Generation of Isocyanates.

Alexander A. Vinogradov; Mark D. Simon; Bradley L. Pentelute

A method for chemo- and regioselective conjugation of nucleophiles to fully unprotected peptides and proteins via in situ generation of C-terminal isocyanates is reported. Oxidation of C-terminal peptide hydrazides in aqueous media followed by Curtius rearrangement of acyl azides reliably generates isocyanates, which react with a variety of external nucleophiles, such as hydrazines, hydrazides, aromatic thiols, and hydroxylamines. Multiple peptides and a 53 kDa protein hydrazide were conjugated to different nucleophiles using this reaction.


Proceedings of the National Academy of Sciences of the United States of America | 2018

Xenoprotein engineering via synthetic libraries

Zachary P. Gates; Alexander A. Vinogradov; Anthony J. Quartararo; Anupam Bandyopadhyay; Zi-Ning Choo; Ethan Daniel Evans; Kathryn H. Halloran; Alexander James Mijalis; Surin K. Mong; Mark D. Simon; Eric A. Standley; Evan D. Styduhar; Sarah Z. Tasker; Fayçal Touti; Jessica M. Weber; Jessica L. Wilson; Timothy F. Jamison; Bradley L. Pentelute

Significance Combinatorial protein libraries—prepared via molecular biology-based approaches—are invaluable tools for protein engineering. The inclusion of noncanonical amino acids in such libraries is of considerable interest. However, at present no approach competes with chemical synthesis in terms of the variety and number of noncanonical amino acids that can be simultaneously incorporated into a protein molecule. Here, we describe selection from synthetic libraries as a strategy for protein engineering. The approach enables identification of small (∼30 aa), functional protein variants comprising a virtually unlimited variety of noncanonical amino acids. Increasing the throughput of synthetic library screening, which was achieved through this effort, is anticipated to improve the utility of synthetic libraries for identifying polypeptide-based ligands with de novo function. Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.


Angewandte Chemie | 2013

Enzymatic “Click” Ligation: Selective Cysteine Modification in Polypeptides Enabled by Promiscuous Glutathione S-Transferase†

Chi Zhang; Alexander M. Spokoyny; Yekui Zou; Mark D. Simon; Bradley L. Pentelute


Journal of the American Chemical Society | 2016

d-Amino Acid Scan of Two Small Proteins

Mark D. Simon; Yuta Maki; Alexander A. Vinogradov; Chi Zhang; Hongtao Yu; Yu-Shan Lin; Yasuhiro Kajihara; Bradley L. Pentelute


Organic and Biomolecular Chemistry | 2016

A perfluoroaromatic abiotic analog of H2 relaxin enabled by rapid flow-based peptide synthesis

Tessa Lühmann; Surin K. Mong; Mark D. Simon; Lorenz Meinel; Bradley L. Pentelute


Archive | 2014

Solid phase peptide synthesis processes and associated systems

Mark D. Simon; Bradley L. Pentelute; Andrea Adamo; Patrick L. Heider; Klavs F. Jensen

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Bradley L. Pentelute

Massachusetts Institute of Technology

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Surin K. Mong

Massachusetts Institute of Technology

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Alexander A. Vinogradov

Massachusetts Institute of Technology

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Chi Zhang

Massachusetts Institute of Technology

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Alexander James Mijalis

Massachusetts Institute of Technology

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Andrea Adamo

Massachusetts Institute of Technology

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Klavs F. Jensen

Massachusetts Institute of Technology

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Yekui Zou

Massachusetts Institute of Technology

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Patrick L. Heider

Massachusetts Institute of Technology

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