Journal of Molecular Recognition最新文献

{"title":"Marc van Regenmortel, personal recollections on a forward-thinking editor","authors":"Jean-Luc Pellequer,&nbsp;Eric Westhof","doi":"10.1002/jmr.3080","DOIUrl":"10.1002/jmr.3080","url":null,"abstract":"<p>Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmr.3080","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Marc H. V. van Regenmortel, a virtual friend and a real colleague","authors":"Vladimir N. Uversky","doi":"10.1002/jmr.3079","DOIUrl":"10.1002/jmr.3079","url":null,"abstract":"&lt;p&gt;Unlike Jean-Luc Pellequer and Eric Westhof,&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; who were colleagues of Marc H.V. van Regenmortel, I have never met him in person. However, I can add my voice to the discussion of how contingency or serendipity has led me to productively collaborate with Marc (unfortunately, exclusively in the on-line format), resulting in the publication of a joint paper in 2020.&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; Before moving to this part of my story, a short historical excurse is needed.&lt;/p&gt;&lt;p&gt;My first (once again, exclusively virtual) encounter with Marc took place in 2004, when he played a crucial role in our work on one of the first comprehensive reviews on the roles of intrinsically disordered proteins and regions (IDPs/IDRs) in molecular recognition, regulation, and cell signaling.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; In the middle of 2004, I joined the Center for Computational Biology and Bioinformatics (CCBB) at the Indiana University-Purdue University at Indianapolis (IUPUI) that was created and headed by Prof. A. Keith Dunker, whom I worked with for 6 years on different aspects of the protein intrinsic disorder phenomenon. One of my first projects there was analysis of the then-available literature data on the functionality of intrinsic disorder.&lt;/p&gt;&lt;p&gt;By that time, it became clear that although IDPs/IDRs have been mostly ignored by the scientific community since the inception of the lock-and-key model by Hermann Emil Louis Fischer (1852–1919) in 1894,&lt;span&gt;&lt;sup&gt;4, 5&lt;/sup&gt;&lt;/span&gt; many aspects of protein functionality could not be explained using this important model and its associated sequence-structure-function paradigm. In fact, many protein functions do not require specific structures, instead relying on conformational flexibility, and as a result, many biologically active proteins (or protein regions) do not have unique structures, instead being intrinsically disordered.&lt;span&gt;&lt;sup&gt;6-15&lt;/sup&gt;&lt;/span&gt; However, the concept of functional disorder was still met with strong skepticism by the scientific community, especially by those who worked in structural biology.&lt;/p&gt;&lt;p&gt;This brings us to my first example of Marc-centric contingency or serendipity. When Keith contacted Marc to check if the manuscript we were working on would fit the scope of the Journal of Molecular Recognition, to our big surprise, we received very enthusiastic support. Those times were still the early days of protein intrinsic disorder, and many scientific journals were simply dismissing the idea of functional disorder as nonsensical (as an example, it took more than a year to publish my first paper on this subject (Ref. &lt;span&gt;16&lt;/span&gt;), which was rejected by 14 journals before being eventually accepted by Proteins&lt;span&gt;&lt;sup&gt;7&lt;/sup&gt;&lt;/span&gt;). During the preparation of the manuscript for the Journal of Molecular Recognition, we had a productive exchange with Marc, which was very useful and is reflected in the acknowledgement in the resulting paper that reads “Both A.K.D. and V.N.U. t","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmr.3079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139990347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tenth International AFMBioMed Conference on AFM in Life Sciences and Medicine, August 30–September 2, 2022, Nagoya-Okasaki, Japan","authors":"Takayuki Uchihashi,&nbsp;Felix Rico,&nbsp;Jean-Luc Pellequer","doi":"10.1002/jmr.3077","DOIUrl":"10.1002/jmr.3077","url":null,"abstract":"&lt;p&gt;Founded in June 2006, after a first seminal French-speaking conference held on the topic “Atelier Nanobiosciences: protéines et membranes” in &lt;i&gt;Nîmes&lt;/i&gt; in June 2004, the AFMBioMed Conference brings researchers and students from around the world together to discuss the latest scientific results of atomic force microscopy in life sciences and medicine.&lt;span&gt;&lt;sup&gt;1, 2&lt;/sup&gt;&lt;/span&gt; A full account of the AFMBioMed history can be found here.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; AFMBioMed organized its first international meeting in &lt;i&gt;Barcelona&lt;/i&gt;, Spain, in spring 2007&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; and this was followed, at 18-month intervals, by &lt;i&gt;Monterey&lt;/i&gt;, CA, USA, in fall 2008,&lt;span&gt;&lt;sup&gt;5&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;Crveni otok&lt;/i&gt; (Red Island) near the Adriatic City of Rovinj, Croatia, in spring 2010,&lt;span&gt;&lt;sup&gt;6&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;Paris&lt;/i&gt; in summer 2011,&lt;span&gt;&lt;sup&gt;7&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;Shanghai&lt;/i&gt; in spring 2013,&lt;span&gt;&lt;sup&gt;8&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;San Diego&lt;/i&gt; in fall 2014,&lt;span&gt;&lt;sup&gt;9&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;Porto&lt;/i&gt; in spring 2016,&lt;span&gt;&lt;sup&gt;10&lt;/sup&gt;&lt;/span&gt; &lt;i&gt;Krakow&lt;/i&gt; in fall 2017,&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; and &lt;i&gt;Münster&lt;/i&gt; in fall 2019.&lt;span&gt;&lt;sup&gt;11&lt;/sup&gt;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;Members of the scientific committee for the tenth edition of the AFMBioMed meeting in Nagoya-Okasaki, Japan, in summer 2022 include past and present organizers &lt;i&gt;Takayuki Uchihashi&lt;/i&gt; (Nagoya University, Japan), &lt;i&gt;Hermann Schillers&lt;/i&gt; (University of Münster, Germany), &lt;i&gt;Malgorzata Lekka&lt;/i&gt; (Polish Academy of Sciences, Poland), &lt;i&gt;Susana R. Sousa&lt;/i&gt; (i3S|INEB, Porto, Portugal), &lt;i&gt;Adam Engler&lt;/i&gt; (UCSD, San Diego, USA), &lt;i&gt;Jun Hu&lt;/i&gt; (SINAP, Shanghai, China), &lt;i&gt;Sanjay Kumar&lt;/i&gt; (University of California, Berkeley, USA), &lt;i&gt;Daniel Navajas&lt;/i&gt; (Universitat de Barcelona, Barcelona, Spain), &lt;i&gt;Simon Scheuring&lt;/i&gt; (Institut National de la Santé et de la Recherche Médicale (INSERM) U1006, Marseille, France), &lt;i&gt;Vesna Svetlicic&lt;/i&gt; (Rudjer Boskovic Institute, Zagreb, Croatia), the original founders of the conference &lt;i&gt;Pierre Parot&lt;/i&gt; (IACA) and &lt;i&gt;Jean-Luc Pellequer&lt;/i&gt; (CEA/DRF, Institut de Biologie Structurale, Grenoble, France), as well as the four invited chairs: &lt;i&gt;Alice Pyne&lt;/i&gt; (Sheffield University, UK), &lt;i&gt;Felix Rico&lt;/i&gt; (Aix-Marseille University—INSERM, France), &lt;i&gt;Takaharu Okajima&lt;/i&gt; (Hokkaido University, Japan), and &lt;i&gt;Noriyuki Kodera&lt;/i&gt; (Kanazawa University, Japan).&lt;/p&gt;&lt;p&gt;The 10th AFMBioMed was scheduled as a landmark conference. Despite the round number 10, it was the last conference organized with a single AFM sponsor (more below). It should have been the last conference that Pierre Parot, the co-founder of AFMBioMed, would participate in. At the end of the 9th conference in Münster, the 10th AFMBioMed conference was initially planned for spring 2021, the cherry blossom season in Japan. Unfortunately, the COVID-19 pandemic modified our plan. The conference was postponed every 6 months while waiting for the reopening of travel to Japan (as well as other countries). In early 2022, the organi","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmr.3077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139983169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Utilizing fab fragment-conjugated surface plasmon resonance-based biosensor for detection of Salmonella Enteritidis","authors":"Esma Eser,&nbsp;Okan Öner Ekiz,&nbsp;H. İbrahim Ekiz","doi":"10.1002/jmr.3078","DOIUrl":"10.1002/jmr.3078","url":null,"abstract":"<p>Although antibodies, a key element of biorecognition, are frequently used as biosensor probes, the use of these large molecules can lead to adverse effects. Fab fragments can be reduced to allow proper antigen-binding orientation via thiol groups containing Fab sites that can directly penetrate Au sites chemically. In this study, the ability of the surface plasmon resonance (SPR) sensor to detect <i>Salmonella</i> was studied. Tris(2-carboxyethyl)phosphine was used as a reducing agent to obtain half antibody fragments. Sensor surface was immobilized with antibody, and bacteria suspensions were injected from low to high concentrations. Response units were changed by binding first reduced antibody fragments, then bacteria. The biosensor was able to determine the bacterial concentrations between 10³ and 10⁸ CFU/mL. Based on these results, the half antibody fragmentation method can be generalized for faster, label-free, sensitive, and selective detection of other bacteria species.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139940083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications","authors":"Pratik Singh,&nbsp;Priyanka Gopi,&nbsp;Majji Sai Sudha Rani,&nbsp;Shweta Singh,&nbsp;Prateek Pandya","doi":"10.1002/jmr.3076","DOIUrl":"10.1002/jmr.3076","url":null,"abstract":"<p>Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics–Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139746758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of steric hindrance effect on the interactions between four alkaloids and HSA by isothermal titration calorimetry and molecular docking","authors":"Xinluan Lv,&nbsp;Wenjin Li,&nbsp;Miao Zhang,&nbsp;Ruiyong Wang,&nbsp;Junbiao Chang","doi":"10.1002/jmr.3075","DOIUrl":"10.1002/jmr.3075","url":null,"abstract":"<p>The binding of four alkaloids with human serum albumin (HSA) was investigated by isothermal titration calorimetry (ITC), spectroscopy and molecular docking techniques. The findings demonstrated that theophylline or caffeine can bind to HAS, respectively. The number of binding sites and binding constants are obtained. The binding mode is a static quenching process. The effects of steric hindrance, temperature, salt concentration and buffer solution on the binding indicated that theophylline and HSA have higher binding affinity than caffeine. The fluorescence and ITC results showed that the interaction between HSA and theophylline or caffeine is an entropy-driven spontaneous exothermic process. The hydrophobic force was the primary driving factor. The experimental results were consistent with the molecular docking data. Based on the molecular structures of the four alkaloids, steric hindrance might be a major factor in the binding between HSA and these four alkaloids. This study elucidates the mechanism of interactions between four alkaloids and HSA.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spectroscopic, computational, cytotoxicity, and docking studies of 6-bromobenzimidazole as anti-breast cancer agent","authors":"V. S. Kunjumol,&nbsp;S. Jeyavijayan,&nbsp;S. Sumathi,&nbsp;N. Karthik","doi":"10.1002/jmr.3074","DOIUrl":"10.1002/jmr.3074","url":null,"abstract":"<p>6-Bromobenzimidazole (6BBZ) has been calculated in this study utilizing the 6-311++G(d,p) basis set and the Becke-3-Lee-Yang-Parr density functional approaches. The basic frequencies and geometric optimization are known. FTIR, FT-Raman, and UV–Vis spectra of the substance are compared between its computed and observed values. The energy gap between highest occupied molecular orbital–lowest unoccupied molecular orbital and molecule electrostatic potentials has been represented by charge density distributions that may be associated with the biological response. Time-dependent density functional theory calculations in the gas phase and dimethyl sulfoxide were carried out to ascertain the electronic properties and energy gap values using the same basis set. Molecular orbital contributions are investigated using the overlap population, partial, and total densities of states. Natural bond analysis was found to have strong electron delocalization by means of π(C4–C9) → π*(C5–C6), LP (N1) → π*(C7–C8), and LP(Br12) → π*(C5–C6) interactions. The Fukui function and Mulliken analysis have been explored on the atomic charges of the molecule. The nuclear magnetic resonance chemical shifts for ¹H and ¹³C have been computed using the gauge-independent atomic orbital technique. With the highest binding affinity (−6.2 kcal mol⁻¹) against estrogen sulfotransferase receptor (PDB ID: 1AQU) and low IC₅₀ value of 17.23 μg/mL, 6BBZ demonstrated potent action against the MCF-7 breast cancer cell line. Studies on the antibacterial activity and ADMET prediction of the molecule have also been carried out.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune infiltration is associated with pan-cancer prognostic biomarker RING finger protein 187","authors":"Xin-Tong Fan,&nbsp;Bing-Fang Gao,&nbsp;Xiao-Fei Wang,&nbsp;Kai Zhou,&nbsp;Ying Zhao,&nbsp;Jie Yuan","doi":"10.1002/jmr.3071","DOIUrl":"10.1002/jmr.3071","url":null,"abstract":"<p>Cancer is associated with the highest mortality rate globally. While life-saving screening and treatments exist, better awareness is needed. RNF187, an E3 ligase regulating biological processes, belongs to the RING domain-containing E3 ligase family. RNF187 may serve as an oncogene due to abnormal expression in tumors. However, its association with immune infiltration and prognosis across various cancers remains unclear. We searched several databases including TCGA, GTE x, CCLE, TIMER, and GSEA. R software was used to evaluate RNF187 differential expression, survival, pathology stage, DNA methylation, tumor mutational burden (TMB), microsatellite instability (MSI), gene co-expression analysis, mismatch repairs (MMRs), tumor microenvironment (TME), and immune cell infiltration. Clinicopathological data were collected, and immunohistochemistry was used to verify RNF187 expression in tumor tissues. RNF187 expression was up-regulated in various cancers compared to that in normal tissues and associated with poor patient outcomes. Dysregulation of RNF187 expression in multiple cancer types was strongly correlated with DNA methylation, MMR, MSI, and TMB. RNF187 could interact with different immune cells in cancers. Biomarkers associated with RNF187 may be helpful for prognosis and immunology in treating pan-cancer patients.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nucleic acid-based electrochemical biosensor for detection of influenza B by gold nanoparticles","authors":"Isar Yahyavi,&nbsp;Fahime Edalat,&nbsp;Neda Pirbonyeh,&nbsp;Arash Letafati,&nbsp;Naghmeh Sattarahmady,&nbsp;Hossein Heli,&nbsp;Afagh Moattari","doi":"10.1002/jmr.3073","DOIUrl":"10.1002/jmr.3073","url":null,"abstract":"<p>The influenza virus is a pervasive pathogen that exhibits increased prevalence during colder seasons, resulting in a significant annual occurrence of infections. Notably, pharmaceutical interventions effective against influenza A strains often exhibit limited efficacy against influenza B variants. Against this backdrop, the need for innovative approaches to accurately and swiftly differentiate and detect influenza B becomes evident. Biosensors play a pivotal role in this detection process, offering rapid, specific, and sensitive identification of the virus, facilitating timely intervention and containment efforts. Oligonucleotide sequences targeting the conserved B/Victoria/2/87 influenza virus NP region were designed. Nasopharyngeal swabs were collected from patients suspected of influenza virus infection, and viral RNA was extracted. RNA quality was assessed through one-step PCR. cDNA synthesis was performed using random hexamers, and real-time PCR quantified the influenza genome. Gold nanoparticles were immobilized on a surface to immobilize the specific DNA probe, and electrochemical hybridization was electrochemically followed. The biosensor exhibited high selectivity and effective distinction of complementary sequences from mismatches and influenza virus cDNA genome. The biosensor successfully detected the influenza B virus genome in real samples. Non-influenza samples yielded no significant hybridization signals. The comparison between the results obtained from the biosensor and real-time PCR revealed full agreement of these methods. The biosensor utilized electrochemical detection of hybridization and proved effective in detecting the influenza B virus genome with high specificity, sensitivity, and selectivity. Comparative analysis with real-time PCR underscored the accuracy and potential applicability of the biosensor in rapid and specific virus detection. This innovative approach holds promise for future diagnostic and epidemiological applications in detecting influenza B virus and other pathogens.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138830115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermodynamic and structural investigation of the interaction of quaternized 2,3-octakis-[(2-mercaptopyridine)phthalocyaninato] copper (II) sulfate (CuPc) with parallel and hybrid type G-quadruplex","authors":"Gamze Şahin,&nbsp;Esra Bağda,&nbsp;Özge Göktuğ Temiz,&nbsp;Efkan Bağda,&nbsp;Ebubekir Ayhan,&nbsp;Mahmut Durmuş","doi":"10.1002/jmr.3072","DOIUrl":"10.1002/jmr.3072","url":null,"abstract":"<p>G-quadruplexes are important drug targets and get attention due to their existence in telomere, ribosomal DNA, promoter regions of some oncogenes, and the untranslated regions of mRNA. Due to the biological roles of G-quadruplexes, investigating of the G-quadruplex–small molecule interaction is essential. The primary motivation for these studies is the possibility of inhibiting cell functions associated with G-quadruplex sequences by binding with small molecules. Targeting the small molecules to desired tissue with the G-quadruplex vehicles is the second important goal of the G-quadruplex–small molecule interaction studies. In the present study, the new peripherally 2-mercaptopyridine octasubstituted copper(II) phthalocyanine and its quaternized derivative <b>(CuPc)</b> were synthesized and characterized by elemental analysis FT-IR, UV–Vis, and mass spectra. The excellent solubility of <b>CuPc</b> in water is essential for its transport in the organism. Because of this feature, its affinity toward G-quadruplex forming aptamers, AS1411, Tel21, and Tel45, was investigated. The UV–Vis spectrophotometric titration data confirmed the prevention of aggregation upon interaction with G-quadruplex, which is very important for biomedical applications. The CD spectroscopic analyses and binding stoichiometry confirmed the “end stacking” model for interaction of AS1411 with <b>CuPc</b>. The interaction of <b>CuPc</b> caused the equilibrium shift from hybrid conformation to antiparallel conformation for Tel21 and Tel45. The isothermal titration calorimeter (ITC) was used for the determination of thermodynamic parameters. The thermodynamic data of the interaction was fitted well with the one-site model. The negative values of Gibbs free energy change confirmed the spontaneous nature of the reactions. Besides, the negative values of enthalpy change and entropy change proved that the nature of processes was “enthalpy driven.” The interaction stoichiometry was 2 for AS1411 and Tel21 and 1.5 for Tel45. The binding constants were 1.3(±0.3) × 10⁵, 3.2(±0.4) × 10⁵, and 1.1(±0.3) × 10⁵ M⁻¹, which were at the level of ethidium bromide intercalation binding constant given in the literature. The DNA polymerase stop assay further supported the interaction of <b>CuPc</b> with G-quadruplex DNA. The experimental results confirm that the <b>CuPc</b> has a potential photosensitizer behaviour for photodynamic therapy.</p>","PeriodicalId":16531,"journal":{"name":"Journal of Molecular Recognition","volume":"37 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138830156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}