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Young Scholars’ Developments in Chemical Biology

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 20829

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Special Issue Editor

Prof. Dr. Seung Bum Park

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Guest Editor

Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Interests: chemical biology; molecular diversity; drug discovery; bioimaging and high throughput/high content screening; target identification/validation; chemical probes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Chemical biology is an interdisciplinary research area spanning the fields of chemistry and biology, heading toward the development of new strategies to cure and diagnose human diseases. Chemical biologists focus on understanding the fundamental mechanisms of various biological processes at the molecular level. This knowledge can be used to control and modulate these biological processes, especially disease-relevant biological processes, which makes chemical biology a perfect area for young scholars to show their creativity and synergy by combining chemical and biological concepts and tools. This Special Issue of Molecules is titled “Young Scholars’ Development in Chemical Biology”. It is my great honor to serve as Guest Editor for this Special Issue. I hope it will provide a playground for young scholars to show their creativity with bold ideas in chemical biology.

Prof. Dr. Seung Bum Park
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

drugs and small molecules
bio-orthogonal chemistry
proteins
phenotypic screening
nucleic acids
sensing and imaging

Published Papers (5 papers)

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Research

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10 pages, 1826 KiB

Open AccessArticle

Establishing a Klebsiella pneumoniae-Based Cell-Free Protein Synthesis System

by Chen Yang, Miaomiao Yang, Wanhua Zhao, Yue Ding, Yu Wang and Jian Li

Molecules 2022, 27(15), 4684; https://doi.org/10.3390/molecules27154684 - 22 Jul 2022

Cited by 6 | Viewed by 2114

Abstract

Cell-free protein synthesis (CFPS) systems are emerging as powerful platforms for in vitro protein production, which leads to the development of new CFPS systems for different applications. To expand the current CFPS toolkit, here we develop a novel CFPS system derived from a chassis microorganism Klebsiella pneumoniae, an important industrial host for heterologous protein expression and the production of many useful chemicals. First, we engineered the K. pneumoniae strain by deleting a capsule formation-associated wzy gene. This capsule-deficient strain enabled easy collection of the cell biomass for preparing cell extracts. Then, we optimized the procedure of cell extract preparation and the reaction conditions for CFPS. Finally, the optimized CFPS system was able to synthesize a reporter protein (superfolder green fluorescent protein, sfGFP) with a maximum yield of 253 ± 15.79 μg/mL. Looking forward, our K. pneumoniae-based CFPS system will not only expand the toolkit for protein synthesis, but also provide a new platform for constructing in vitro metabolic pathways for the synthesis of high-value chemicals. Full article

(This article belongs to the Special Issue Young Scholars’ Developments in Chemical Biology)

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Review

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12 pages, 1855 KiB

Open AccessReview

Recent Synthetic Biology Approaches for Temperature- and Light-Controlled Gene Expression in Bacterial Hosts

by Jongdoo Choi, Jiyeun Ahn, Jieun Bae and Minseob Koh

Molecules 2022, 27(20), 6798; https://doi.org/10.3390/molecules27206798 - 11 Oct 2022

Cited by 2 | Viewed by 2926

Abstract

The expression of genes of interest (GOI) can be initiated by providing external stimuli such as temperature shifts and light irradiation. The application of thermal or light stimuli triggers structural changes in stimuli-sensitive biomolecules within the cell, thereby inducing or repressing gene expression. Over the past two decades, several groups have reported genetic circuits that use natural or engineered stimuli-sensitive modules to manipulate gene expression. Here, we summarize versatile strategies of thermosensors and light-driven systems for the conditional expression of GOI in bacterial hosts. Full article

(This article belongs to the Special Issue Young Scholars’ Developments in Chemical Biology)

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23 pages, 7140 KiB

Open AccessFeature PaperReview

Discovery of E3 Ligase Ligands for Target Protein Degradation

by Jaeseok Lee, Youngjun Lee, Young Mee Jung, Ju Hyun Park, Hyuk Sang Yoo and Jongmin Park

Molecules 2022, 27(19), 6515; https://doi.org/10.3390/molecules27196515 - 02 Oct 2022

Cited by 21 | Viewed by 10077

Abstract

Target protein degradation has emerged as a promising strategy for the discovery of novel therapeutics during the last decade. Proteolysis-targeting chimera (PROTAC) harnesses a cellular ubiquitin-dependent proteolysis system for the efficient degradation of a protein of interest. PROTAC consists of a target protein ligand and an E3 ligase ligand so that it enables the target protein degradation owing to the induced proximity with ubiquitin ligases. Although a great number of PROTACs has been developed so far using previously reported ligands of proteins for their degradation, E3 ligase ligands have been mostly limited to either CRBN or VHL ligands. Those PROTACs showed their limitation due to the cell type specific expression of E3 ligases and recently reported resistance toward PROTACs with CRBN ligands or VHL ligands. To overcome these hurdles, the discovery of various E3 ligase ligands has been spotlighted to improve the current PROTAC technology. This review focuses on currently reported E3 ligase ligands and their application in the development of PROTACs. Full article

(This article belongs to the Special Issue Young Scholars’ Developments in Chemical Biology)

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23 pages, 3768 KiB

Open AccessReview

Small Molecules for Enhancing the Precision and Safety of Genome Editing

by Siyoon Shin, Seeun Jang and Donghyun Lim

Molecules 2022, 27(19), 6266; https://doi.org/10.3390/molecules27196266 - 23 Sep 2022

Cited by 6 | Viewed by 2458

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities. Full article

(This article belongs to the Special Issue Young Scholars’ Developments in Chemical Biology)

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18 pages, 5713 KiB

Open AccessReview

Chemical Modulators for Targeting Autism Spectrum Disorders: From Bench to Clinic

by Songhyun Lim and Sanghee Lee

Molecules 2022, 27(16), 5088; https://doi.org/10.3390/molecules27165088 - 10 Aug 2022

Cited by 4 | Viewed by 2699

Abstract

Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by diverse behavioral symptoms such as repetitive behaviors, social deficits, anxiety, hyperactivity, and irritability. Despite their increasing incidence, the specific pathological mechanisms of ASD are still unknown, and the degree and types of symptoms that vary from patient to patient make it difficult to develop drugs that target the core symptoms of ASD. Although various atypical antipsychotics and antidepressants have been applied to regulate ASD symptoms, these drugs can only alleviate the symptoms and do not target the major causes. Therefore, development of novel drugs targeting factors directly related to the onset of ASD is required. Among the various factors related to the onset of ASD, several chemical modulators to treat ASD, focused on serotonin (5-hydroxytryptamine, 5-HT) and glutamate receptors, microbial metabolites, and inflammatory cytokines, are explored in this study. In particular, we focus on the chemical drugs that have improved various aspects of ASD symptoms in animal models and in clinical trials for various ages of patients with ASD. Full article

(This article belongs to the Special Issue Young Scholars’ Developments in Chemical Biology)

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