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Feature Review Papers in Chemical Biology
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Feature Review Papers in Chemical Biology

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

Deadline for manuscript submissions: closed (1 September 2021) | Viewed by 68634

Special Issue Editors

Prof. Dr. Akinori Kuzuya

E-Mail Website
Guest Editor
Organization for Research and Development of Innovative Science and Technology (ORDIST), Kansai University, Suita, Osaka 564-8680, Japan
Interests: nucleic acid chemistry; DNA nanotechnology; supramolecular chemistry; molecular machines; molecular robotics; molecular technology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Roland J. Pieters

E-Mail Website
Guest Editor
Division of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
Interests: protein-carbohydrate interactions; lectins; glycosidases; carbohydrate microarrays; multivalency; bacterial adhesion; viral adhesion; O-GlcNAcylation
Special Issues, Collections and Topics in MDPI journals
Dr. Takuya Terai

E-Mail Website
Guest Editor
Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
Interests: chemical biology; fluorescence/luminescence probe; fluorescence imaging; high-throughput screening; directed molecular evolution; peptide aptamer
Dr. Eylon Yavin

E-Mail Website
Guest Editor
The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 9112102, Israel
Interests: PNA (peptide nucleic acid); FIT-PNA (forced-intercalation-PNA); CPP (cell penetrating peptides); RNA diagnostics, antisense
Special Issues, Collections and Topics in MDPI journals
Dr. Alejandro Samhan-Arias

E-Mail Website1 Website2
Guest Editor
Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), C/Arturo Duperier 4, 28029-Madrid, Spain
Interests: free radical biology; reactive oxygen species; reactive nitrogen species; peroxidases; NADH oxidases; lipidomics; intrinsically disordered proteins; neurodegenerative diseases; redox biomedicine
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Isao Kii

E-Mail Website
Guest Editor
Laboratory for Drug Target Research, Faculty & Graduate School of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan
Interests: kinase, protein folding; folding intermediate; activation mechanism; autophosphorylation; chaperone; structural analysis; protein quality control; ubiquitin proteasome pathway; Small molecule inhibitor; neurogenesis; intellectual disability; down syndrome; autism spectrum disorders; click reaction; protein modification; immuno-PET imaging

Special Issue Information

Dear Colleagues,

In this Special Issue, ‘Feature Review Papers in Chemical Biology’, we aim to publish review articles within the field of Chemical Biology. While the definition of the field overlaps with medicinal and bioorganic chemistry, distinct aspects can be defined which earmark studies for this field at the interface of Chemistry and Biology. Molecules are used for interference with or visualize biological systems at the molecular level, which can lead to new insights into these systems and their biological mechanisms or provide tools for their manipulation. Studies must include bioactive synthesized or isolated compounds or probes to realize the above goals. Studies in which compounds are described that capture or detect specific components in a biological context are also of interest.

Prof. Akinori Kuzuya
Prof. Dr. Roland J. Pieters
Dr. Takuya Terai
Prof. Eylon Yavin
Dr. Alejandro Samhan-Arias
Dr. Isao Kii
Guest Editors

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

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.

Published Papers (15 papers)

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Review

14 pages, 1066 KiB  
Review
Chemical Approaches for Studying the Biology and Pharmacology of Membrane Transporters: The Histidine/Large Amino Acid Transporter SLC7A5 as a Benchmark
by Mariafrancesca Scalise, Raffaella Scanga, Lara Console, Michele Galluccio, Lorena Pochini and Cesare Indiveri
Molecules 2021, 26(21), 6562; https://doi.org/10.3390/molecules26216562 - 29 Oct 2021
Cited by 6 | Viewed by 2697
Abstract
The localization of membrane transporters at the forefront of natural barriers makes these proteins very interesting due to their involvement in the absorption and distribution of nutrients and xenobiotics, including drugs. Over the years, structure/function relationship studies have been performed employing several strategies, [...] Read more.
The localization of membrane transporters at the forefront of natural barriers makes these proteins very interesting due to their involvement in the absorption and distribution of nutrients and xenobiotics, including drugs. Over the years, structure/function relationship studies have been performed employing several strategies, including chemical modification of exposed amino acid residues. These approaches are very meaningful when applied to membrane transporters, given that these proteins are characterized by both hydrophobic and hydrophilic domains with a different degree of accessibility to employed chemicals. Besides basic features, the chemical targeting approaches can disclose information useful for pharmacological applications as well. An eminent example of this picture is the histidine/large amino acid transporter SLC7A5, known as LAT1 (Large Amino Acid Transporter 1). This protein is crucial in cell life because it is responsible for mediating the absorption and distribution of essential amino acids in peculiar body districts, such as the blood brain barrier and placenta. Furthermore, LAT1 can recognize a large variety of molecules of pharmacological interest and is also considered a hot target for drugs due to its over-expression in virtually all human cancers. Therefore, it is not surprising that the chemical targeting approach, coupled with bioinformatics, site-directed mutagenesis and transport assays, proved fundamental in describing features of LAT1 such as the substrate binding site, regulatory domains and interactions with drugs that will be discussed in this review. The results on LAT1 can be considered to have general applicability to other transporters linked with human diseases. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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23 pages, 7073 KiB  
Review
Recognition of Chiral Carboxylates by Synthetic Receptors
by Patryk Niedbała, Kajetan Dąbrowa, Sylwia Wasiłek and Janusz Jurczak
Molecules 2021, 26(21), 6417; https://doi.org/10.3390/molecules26216417 - 24 Oct 2021
Cited by 8 | Viewed by 1954
Abstract
Recognition of anionic species plays a fundamental role in many essential chemical, biological, and environmental processes. Numerous monographs and review papers on molecular recognition of anions by synthetic receptors reflect the continuing and growing interest in this area of supramolecular chemistry. However, despite [...] Read more.
Recognition of anionic species plays a fundamental role in many essential chemical, biological, and environmental processes. Numerous monographs and review papers on molecular recognition of anions by synthetic receptors reflect the continuing and growing interest in this area of supramolecular chemistry. However, despite the enormous progress made over the last 20 years in the design of these molecules, the design of receptors for chiral anions is much less developed. Chiral recognition is one of the most subtle types of selectivity, and it requires very precise spatial organization of the receptor framework. At the same time, this phenomenon commonly occurs in many processes present in nature, often being their fundamental step. For these reasons, research directed toward understanding the chiral anion recognition phenomenon may lead to the identification of structural patterns that enable increasingly efficient receptor design. In this review, we present the recent progress made in the area of synthetic receptors for biologically relevant chiral carboxylates. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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21 pages, 1814 KiB  
Review
Natural Polyphenols as Immunomodulators to Rescue Immune Response Homeostasis: Quercetin as a Research Model against Severe COVID-19
by Roberta Bernini and Francesca Velotti
Molecules 2021, 26(19), 5803; https://doi.org/10.3390/molecules26195803 - 25 Sep 2021
Cited by 14 | Viewed by 3228
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2 and is leading to the worst health crisis of this century. It emerged in China during late 2019 and rapidly spread all over the world, producing a broad spectrum of clinical disease severity, ranging from asymptomatic [...] Read more.
The COVID-19 pandemic is caused by SARS-CoV-2 and is leading to the worst health crisis of this century. It emerged in China during late 2019 and rapidly spread all over the world, producing a broad spectrum of clinical disease severity, ranging from asymptomatic infection to death (4.3 million victims so far). Consequently, the scientific research is devoted to investigating the mechanisms of COVID-19 pathogenesis to both identify specific therapeutic drugs and develop vaccines. Although immunological mechanisms driving COVID-19 pathogenesis are still largely unknown, new understanding has emerged about the innate and adaptive immune responses elicited in SARS-CoV-2 infection, which are mainly focused on the dysregulated inflammatory response in severe COVID-19. Polyphenols are naturally occurring products with immunomodulatory activity, playing a relevant role in reducing inflammation and preventing the onset of serious chronic diseases. Mainly based on data collected before the appearance of SARS-CoV-2, polyphenols have been recently suggested as promising agents to fight COVID-19, and some clinical trials have already been approved with polyphenols to treat COVID-19. The aim of this review is to analyze and discuss the in vitro and in vivo research on the immunomodulatory activity of quercetin as a research model of polyphenols, focusing on research that addresses issues related to the dysregulated immune response in severe COVID-19. From this analysis, it emerges that although encouraging data are present, they are still insufficient to recommend polyphenols as potential immunomodulatory agents against COVID-19. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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34 pages, 8654 KiB  
Review
Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation
by Laura Márquez-Cantudo, Ana Ramos, Claire Coderch and Beatriz de Pascual-Teresa
Molecules 2021, 26(18), 5606; https://doi.org/10.3390/molecules26185606 - 15 Sep 2021
Cited by 3 | Viewed by 3886
Abstract
Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting [...] Read more.
Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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12 pages, 972 KiB  
Review
Preclinical Testing of Radiopharmaceuticals for the Detection and Characterization of Osteomyelitis: Experiences from a Porcine Model
by Aage Kristian Olsen Alstrup, Svend Borup Jensen, Ole Lerberg Nielsen, Lars Jødal and Pia Afzelius
Molecules 2021, 26(14), 4221; https://doi.org/10.3390/molecules26144221 - 12 Jul 2021
Cited by 4 | Viewed by 2370
Abstract
The development of new and better radioactive tracers capable of detecting and characterizing osteomyelitis is an ongoing process, mainly because available tracers lack selectivity towards osteomyelitis. An integrated part of developing new tracers is the performance of in vivo tests using appropriate animal [...] Read more.
The development of new and better radioactive tracers capable of detecting and characterizing osteomyelitis is an ongoing process, mainly because available tracers lack selectivity towards osteomyelitis. An integrated part of developing new tracers is the performance of in vivo tests using appropriate animal models. The available animal models for osteomyelitis are also far from ideal. Therefore, developing improved animal osteomyelitis models is as important as developing new radioactive tracers. We recently published a review on radioactive tracers. In this review, we only present and discuss osteomyelitis models. Three ethical aspects (3R) are essential when exposing experimental animals to infections. Thus, we should perform experiments in vitro rather than in vivo (Replacement), use as few animals as possible (Reduction), and impose as little pain on the animal as possible (Refinement). The gain for humans should by far exceed the disadvantages for the individual experimental animal. To this end, the translational value of animal experiments is crucial. We therefore need a robust and well-characterized animal model to evaluate new osteomyelitis tracers to be sure that unpredicted variation in the animal model does not lead to a misinterpretation of the tracer behavior. In this review, we focus on how the development of radioactive tracers relies heavily on the selection of a reliable animal model, and we base the discussions on our own experience with a porcine model. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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22 pages, 1577 KiB  
Review
Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials
by Luigi Di Costanzo and Barbara Panunzi
Molecules 2021, 26(10), 2952; https://doi.org/10.3390/molecules26102952 - 16 May 2021
Cited by 32 | Viewed by 5848
Abstract
Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors [...] Read more.
Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors are gaining widespread attention as non-destructive tools, visible to the human eye, that are capable of a real-time and in-situ response. Optical “visual” sensors are expanding researchers’ interests in many chemical contexts and are routinely used for biological, environmental, and medical applications. In this review we provide an overview of trending colorimetric, fluorescent, or dual-mode responsive visual pH sensors. These sensors include molecular synthetic organic sensors, metal organic frameworks (MOF), engineered sensing nanomaterials, and bioengineered sensors. We review different typological chemical entities of visual pH sensors, three-dimensional structures, and signaling mechanisms for pH sensing and applications; developed in the past five years. The progression of this review from simple organic molecules to biological macromolecules seeks to benefit beginners and scientists embarking on a project of pH sensing development, who needs background information and a quick update on advances in the field. Lessons learned from these tools will aid pH determination projects and provide new ways of thinking for cell bioimaging or other cutting-edge in vivo applications. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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37 pages, 2220 KiB  
Review
Elucidating Role of Reactive Oxygen Species (ROS) in Cisplatin Chemotherapy: A Focus on Molecular Pathways and Possible Therapeutic Strategies
by Sepideh Mirzaei, Kiavash Hushmandi, Amirhossein Zabolian, Hossein Saleki, Seyed Mohammad Reza Torabi, Adnan Ranjbar, SeyedHesam SeyedSaleh, Seyed Omid Sharifzadeh, Haroon Khan, Milad Ashrafizadeh, Ali Zarrabi and Kwang-seok Ahn
Molecules 2021, 26(8), 2382; https://doi.org/10.3390/molecules26082382 - 19 Apr 2021
Cited by 63 | Viewed by 6595
Abstract
The failure of chemotherapy is a major challenge nowadays, and in order to ensure effective treatment of cancer patients, it is of great importance to reveal the molecular pathways and mechanisms involved in chemoresistance. Cisplatin (CP) is a platinum-containing drug with anti-tumor activity [...] Read more.
The failure of chemotherapy is a major challenge nowadays, and in order to ensure effective treatment of cancer patients, it is of great importance to reveal the molecular pathways and mechanisms involved in chemoresistance. Cisplatin (CP) is a platinum-containing drug with anti-tumor activity against different cancers in both pre-clinical and clinical studies. However, drug resistance has restricted its potential in the treatment of cancer patients. CP can promote levels of free radicals, particularly reactive oxygen species (ROS) to induce cell death. Due to the double-edged sword role of ROS in cancer as a pro-survival or pro-death mechanism, ROS can result in CP resistance. In the present review, association of ROS with CP sensitivity/resistance is discussed, and in particular, how molecular pathways, both upstream and downstream targets, can affect the response of cancer cells to CP chemotherapy. Furthermore, anti-tumor compounds, such as curcumin, emodin, chloroquine that regulate ROS and related molecular pathways in increasing CP sensitivity are described. Nanoparticles can provide co-delivery of CP with anti-tumor agents and by mediating photodynamic therapy, and induce ROS overgeneration to trigger CP sensitivity. Genetic tools, such as small interfering RNA (siRNA) can down-regulate molecular pathways such as HIF-1α and Nrf2 to promote ROS levels, leading to CP sensitivity. Considering the relationship between ROS and CP chemotherapy, and translating these findings to clinic can pave the way for effective treatment of cancer patients. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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14 pages, 2067 KiB  
Review
Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets
by Yusuke Hosoya and Junko Ohkanda
Molecules 2021, 26(8), 2118; https://doi.org/10.3390/molecules26082118 - 07 Apr 2021
Cited by 17 | Viewed by 3809
Abstract
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of [...] Read more.
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid–liquid phase separations—which critically involve both intermolecular interactions between IDPs and their posttranslational modification—are analyzed to understand the potential of IDPs as new drug targets. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
21 pages, 23127 KiB  
Review
Molecular Design of d-Luciferin-Based Bioluminescence and 1,2-Dioxetane-Based Chemiluminescence Substrates for Altered Output Wavelength and Detecting Various Molecules
by Hideo Takakura
Molecules 2021, 26(6), 1618; https://doi.org/10.3390/molecules26061618 - 15 Mar 2021
Cited by 9 | Viewed by 4627
Abstract
Optical imaging including fluorescence and luminescence is the most popular method for the in vivo imaging in mice. Luminescence imaging is considered to be superior to fluorescence imaging due to the lack of both autofluorescence and the scattering of excitation light. To date, [...] Read more.
Optical imaging including fluorescence and luminescence is the most popular method for the in vivo imaging in mice. Luminescence imaging is considered to be superior to fluorescence imaging due to the lack of both autofluorescence and the scattering of excitation light. To date, various luciferin analogs and bioluminescence probes have been developed for deep tissue and molecular imaging. Recently, chemiluminescence probes have been developed based on a 1,2-dioxetane scaffold. In this review, the accumulated findings of numerous studies and the design strategies of bioluminescence and chemiluminescence imaging reagents are summarized. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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16 pages, 2583 KiB  
Review
Druggable Transient Pockets in Protein Kinases
by Koji Umezawa and Isao Kii
Molecules 2021, 26(3), 651; https://doi.org/10.3390/molecules26030651 - 27 Jan 2021
Cited by 15 | Viewed by 5559
Abstract
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of [...] Read more.
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of recombinant enzyme proteins. Non-canonical inhibitors targeting a hidden pocket in a protein have received considerable research attention. Kii and colleagues identified an inhibitor targeting a transient pocket in the kinase DYRK1A during its folding process and termed it FINDY. FINDY exhibits a unique inhibitory profile; that is, FINDY does not inhibit the fully folded form of DYRK1A, indicating that the FINDY-binding pocket is hidden in the folded form. This intriguing pocket opens during the folding process and then closes upon completion of folding. In this review, we discuss previously established kinase inhibitors and their inhibitory mechanisms in comparison with FINDY. We also compare the inhibitory mechanisms with the growing concept of “cryptic inhibitor-binding sites.” These sites are buried on the inhibitor-unbound surface but become apparent when the inhibitor is bound. In addition, an alternative method based on cell-free protein synthesis of protein kinases may allow the discovery of small molecules that occupy these mysterious binding sites. Transitional folding intermediates would become alternative targets in drug discovery, enabling the efficient development of potent kinase inhibitors. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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41 pages, 9257 KiB  
Review
Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors
by Joana N. Martins, João Carlos Lima and Nuno Basílio
Molecules 2021, 26(1), 106; https://doi.org/10.3390/molecules26010106 - 28 Dec 2020
Cited by 21 | Viewed by 4480
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have [...] Read more.
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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16 pages, 1118 KiB  
Review
Photoinduced Endosomal Escape Mechanism: A View from Photochemical Internalization Mediated by CPP-Photosensitizer Conjugates
by Tet Htut Soe, Kazunori Watanabe and Takashi Ohtsuki
Molecules 2021, 26(1), 36; https://doi.org/10.3390/molecules26010036 - 23 Dec 2020
Cited by 16 | Viewed by 3613
Abstract
Endosomal escape in cell-penetrating peptide (CPP)-based drug/macromolecule delivery systems is frequently insufficient. The CPP-fused molecules tend to remain trapped inside endosomes and end up being degraded rather than delivered into the cytosol. One of the methods for endosomal escape of CPP-fused molecules is [...] Read more.
Endosomal escape in cell-penetrating peptide (CPP)-based drug/macromolecule delivery systems is frequently insufficient. The CPP-fused molecules tend to remain trapped inside endosomes and end up being degraded rather than delivered into the cytosol. One of the methods for endosomal escape of CPP-fused molecules is photochemical internalization (PCI), which is based on the use of light and a photosensitizer and relies on photoinduced endosomal membrane destabilization to release the cargo molecule. Currently, it remains unclear how this delivery strategy behaves after photostimulation. Recent findings, including our studies using CPP-cargo-photosensitizer conjugates, have shed light on the photoinduced endosomal escape mechanism. In this review, we discuss the structural design of CPP-photosensitizer and CPP-cargo-photosensitizer conjugates, and the PCI mechanism underlying their application. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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21 pages, 2458 KiB  
Review
Bioorthogonal Reactions in Activity-Based Protein Profiling
by Steven H. L. Verhelst, Kimberly M. Bonger and Lianne I. Willems
Molecules 2020, 25(24), 5994; https://doi.org/10.3390/molecules25245994 - 18 Dec 2020
Cited by 13 | Viewed by 5048
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase [...] Read more.
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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52 pages, 19764 KiB  
Review
Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes
by Sascha G. Keller, Mako Kamiya and Yasuteru Urano
Molecules 2020, 25(24), 5964; https://doi.org/10.3390/molecules25245964 - 16 Dec 2020
Cited by 26 | Viewed by 6590
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10′. After a short introduction, we [...] Read more.
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10′. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure–behavior relationship including novel computational approaches. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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25 pages, 2004 KiB  
Review
Targeting Lipid Peroxidation for Cancer Treatment
by Sofia M. Clemente, Oscar H. Martínez-Costa, Maria Monsalve and Alejandro K. Samhan-Arias
Molecules 2020, 25(21), 5144; https://doi.org/10.3390/molecules25215144 - 05 Nov 2020
Cited by 52 | Viewed by 5780
Abstract
Cancer is one of the highest prevalent diseases in humans. The chances of surviving cancer and its prognosis are very dependent on the affected tissue, body location, and stage at which the disease is diagnosed. Researchers and pharmaceutical companies worldwide are pursuing many [...] Read more.
Cancer is one of the highest prevalent diseases in humans. The chances of surviving cancer and its prognosis are very dependent on the affected tissue, body location, and stage at which the disease is diagnosed. Researchers and pharmaceutical companies worldwide are pursuing many attempts to look for compounds to treat this malignancy. Most of the current strategies to fight cancer implicate the use of compounds acting on DNA damage checkpoints, non-receptor tyrosine kinases activities, regulators of the hedgehog signaling pathways, and metabolic adaptations placed in cancer. In the last decade, the finding of a lipid peroxidation increase linked to 15-lipoxygenases isoform 1 (15-LOX-1) activity stimulation has been found in specific successful treatments against cancer. This discovery contrasts with the production of other lipid oxidation signatures generated by stimulation of other lipoxygenases such as 5-LOX and 12-LOX, and cyclooxygenase (COX-2) activities, which have been suggested as cancer biomarkers and which inhibitors present anti-tumoral and antiproliferative activities. These findings support the previously proposed role of lipid hydroperoxides and their metabolites as cancer cell mediators. Depletion or promotion of lipid peroxidation is generally related to a specific production source associated with a cancer stage or tissue in which cancer originates. This review highlights the potential therapeutical use of chemical derivatives to stimulate or block specific cellular routes to generate lipid hydroperoxides to treat this disease. Full article
(This article belongs to the Special Issue Feature Review Papers in Chemical Biology)
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