Review
Chemistry, Physical
Bulti Bakchi, Ambati Dileep Krishna, Ekambarapu Sreecharan, Veeramallu Bala Jaya Ganesh, Muraboina Niharika, Suryadevara Maharshi, Srinivasa Babu Puttagunta, Dilep Kumar Sigalapalli, Richie R. Bhandare, Afzal B. Shaik
Summary: In silico techniques, particularly the SwissADME tool, have gained popularity in small molecule drug discovery. This tool allows for hit generation, interaction pattern determination, and prediction of physicochemical and pharmacokinetic parameters. This article discusses the role of SwissADME in the design and development of anticancer, antitubercular, and antimicrobial agents.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Physical
C. P. Kaushik, Jyoti Sangwan, Raj Luxmi, Devinder Kumar, Deepak Kumar, Ashutosh Das, Ashwani Kumar, Dharmendra Singh
Summary: A series of anticancer and antioxidant compounds were synthesized through click chemistry method, with some compounds showing promising activity against cancer cell lines and strong antioxidant activity. Molecular docking studies revealed high binding affinities of certain compounds, suggesting their potential as future candidates for anticancer treatment. In-silico ADME studies also indicated good dispositional profile and patient compliance of the synthesized compounds.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Medicinal
Jean-Jacques Helesbeux, Laura Carro, Florence O. McCarthy, Vania M. Moreira, Francesca Giuntini, Niamh O'Boyle, Susan E. Matthews, Guelsah Bayraktar, Samuel Bertrand, Christophe Rochais, Pascal Marchand
Summary: The 29th Annual GP(2)A Conference was held virtually this year due to the COVID-19 pandemic, spanning three days and attracting an international delegation of researchers. Keynote lectures, young researcher talks, and flash presentation posters were included in the report, showcasing high-level scientific discussions on cutting-edge advances in pharmaceutical chemistry.
Article
Chemistry, Medicinal
Armin Welker, Christian Kersten, Christin Mueller, Ramakanth Madhugiri, Collin Zimmer, Patrick Mueller, Robert Zimmermann, Stefan Hammerschmidt, Hannah Maus, John Ziebuhr, Christoph Sotriffer, Tanja Schirmeister
Summary: Inhibition of coronavirus-encoded PLpro enzymes is a promising strategy for treating infections by these pathogens. The study identified a noncovalent inhibitor and a new class of potent PL(pro) inhibitors, shedding light on their binding modes and potential inhibitory effects on SARS-CoV-2 replication. Additionally, the structural similarities between target proteases suggest that inhibitors identified against SARS-CoV PLpro could be valuable for developing pan-coronaviral inhibitors.
Review
Chemistry, Multidisciplinary
Weihua Chen, Zhen Sun, Lehui Lu
Summary: This review highlights the main drawbacks of current anticancer drugs and the urgency to improve targeting efficacy. It summarizes current targeting strategies and offers guidelines for structure optimization to obtain effective targeting drugs. Additionally, it presents viewpoints on crucial problems and potential challenges in future research on targeted cancer therapy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Nadia A. Khalil, Eman M. Ahmed, Ashraf F. Zaher, Shimaa M. Alhamaky, Nada Osama, Mona S. El-Zoghbi
Summary: New benzothienopyran and benzothienopyranopyrimidine derivatives were synthesized as potential topoisomerase I inhibitors, exhibiting strong cytotoxic activity against human tumor cell lines. Eight compounds demonstrated broad spectrum and potent anticancer efficacy, while three compounds showed excellent inhibitory activity in DNA relaxation assay. Compound 4d arrested cell growth at S phase and demonstrated similar binding pattern to indenoisoquinoline reference drug, indicating its potential as a Topo I inhibitor.
BIOORGANIC CHEMISTRY
(2023)
Review
Infectious Diseases
Shreya Modi, Gajendra Kumar Inwati, Amel Gacem, Shahabe Saquib Abullais, Rajendra Prajapati, Virendra Kumar Yadav, Rabbani Syed, Mohammed S. Alqahtani, Krishna Kumar Yadav, Saiful Islam, Yongtae Ahn, Byong-Hun Jeon
Summary: Nanostructures with particle sizes ranging from 1 to 100 nanometers, known as nanoantibiotics, have emerged as novel antibacterial agents. These nanomaterials show greater antibacterial effects on both Gram-positive and Gram-negative bacteria. They have applications in medical implants, restorative matters, and antibacterial vaccinations. Nanoparticles, with their disrupted antibacterial effects and better biocompatibility, are considered as advanced solution tools for medical science and allied health science.
Article
Multidisciplinary Sciences
Marzieh Sohrabi, Mohammad Nazari Montazer, Sara Moghadam Farid, Nader Tanideh, Mehdi Dianatpour, Ali Moazzam, Kamiar Zomorodian, Somayeh Yazdanpanah, Mehdi Asadi, Samanesadat Hosseini, Mahmood Biglar, Bagher Larijani, Massoud Amanlou, Maliheh Barazandeh Tehrani, Aida Iraji, Mohammad Mahdavi
Summary: The present study synthesized a series of thioquinazolinone derivatives conjugated with nitrothiazolacetamide and investigated their inhibitory activity against urease. Compound 8h exhibited the strongest inhibitory activity and showed high anti-ureolytic activity against two urease-positive microorganisms. Molecular docking study revealed that 8h interacted with multiple residues and demonstrated good hydrophobicity against urease.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Dhananjay D. Jade, Rajan Pandey, Rakesh Kumar, Dinesh Gupta
Summary: In this study, small molecule inhibitors targeting TNF-α were identified using various computational methods. The results showed that these inhibitors had better binding energies compared to known inhibitors and exhibited stable binding with TNF-α protein. Sixteen compounds passed ADMET analysis, indicating their potential for designing future effective TNF-α inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Chemistry, Medicinal
Zhang ChunYan, Yu RuJian, Wang LiQiang, Huang HaiYan, Wang JinTao, Liao XiangWen, Duan XueMin, Xiong YanShi
Summary: This study designed, synthesized, and evaluated four new ruthenium polypyridine complexes modified with 4-tBu-phenyl sulfide. These complexes showed strong antimicrobial activity against Staphylococcus aureus both in vitro and in vivo, making them a potential treatment option for Gram-positive bacterial infections.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Miguel Garcia-Ortegon, Gregor N. C. Simm, Austin J. Tripp, Jose Miguel Hernandez-Lobato, Andreas Bender, Sergio Bacallado
Summary: The field of machine learning for drug discovery is experiencing rapid growth in novel methods. Benchmarking these methods on simple physicochemical properties may not accurately represent the objective functions in drug design. In contrast, molecular docking is a widely used method in drug discovery, but its adoption is hindered by the need for domain knowledge. DOCKSTRING is a bundle that enables meaningful and robust comparison of machine learning models using docking scores. It provides a Python package for easy computation of docking scores, a dataset of docking scores and poses, and pharmaceutically relevant benchmark tasks. The results indicate that docking scores provide a more realistic evaluation objective, making the benchmark tasks more challenging and closely related to real problems in drug discovery.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Virology
Roberto Vazquez, Ernesto Garcia, Pedro Garcia
Summary: Phage-encoded lytic enzymes, or lysins, are a promising alternative to common antibiotics for combating resistant bacterial infections. Research has shown that lysins exhibit different physicochemical properties based on the bacterial hosts they infect, which could lead to new possibilities in antimicrobial drug development.
JOURNAL OF VIROLOGY
(2021)
Review
Chemistry, Medicinal
C. G. Arya, Ramesh Gondru, Yupeng Li, Janardhan Banothu
Summary: This study summarizes the improvement of pharmacokinetic and pharmacodynamic properties of coumarin and benzimidazole compounds through molecular hybridization, and highlights the biological properties and functions of different classes of their hybrids. These hybrids exhibit diverse biological activities, including anticancer, antiviral, antimicrobial effects.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Antti Poso
Summary: WRD5 is a promising target for anticancer drug discovery and plays a vital role in epigenetic regulation. PROTACs offer a new option for biological inactivation of WRD5, and new WRD5 targeting PROTACs introduced in a study make it possible to evaluate WRD5 as a drug target.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Jyoti Rasgania, Renu Gavadia, Komal Jakhar
Summary: The synthesis of a series of N-substituted-2,5-dioxopyrrolidine carboxamides/carbothioamides using microwave irradiation technology under aqueous conditions is reported. Quantum chemical data and chemical reactivity parameters were obtained for the synthesized compounds using DFT calculations. In vitro biological evaluation showed promising antimicrobial potential and radical scavenging ability. Molecular docking simulation revealed favorable binding interactions and good docking score against glucosamine-6-phosphate synthase, suggesting potential as antifungal agents. ADMET prediction and drug likeliness analysis supported the oral bioavailability of the synthesized compounds.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Analytical
Maike Arndt, Marc Rurik, Alissa Drees, Christian Ahlers, Simon Feldmann, Oliver Kohlbacher, Markus Fischer
Summary: This study aimed to predict the geographical origin of almonds using FT-NIR spectroscopy, achieving a mean classification accuracy of 80.3% with the SVM model. By combining Spanish and Italian almonds into a Mediterranean class, the overall classification accuracy increased to up to 88.2%, demonstrating the suitability of NIR screening for determining the geographical origin of almonds.
MICROCHEMICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Marina Creydt, Lea Ludwig, Michael Kohl, Jorg Fromm, Markus Fischer
Summary: The analysis of wood geographical origin using different extraction methods can effectively distinguish the geographic source of wood, helping to prevent illegal logging and timber trade. Multivariate data analysis can extract differences related to geographic origin, and the identification of marker substances reveals metabolic pathways affected by geographical influences.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Medicinal
Henni-Karoliina Ropponen, Chantal D. Bader, Eleonora Diamanti, Boris Illarionov, Matthias Rottmann, Markus Fischer, Matthias Witschel, Rolf Mueller, Anna K. H. Hirsch
Summary: This study presents a case of chemical decomposition of 2-aminothiazole 1 in DMSO, leading to loss of reproducible biological activities. Through solvent- and temperature-dependent studies, oxygenated and dimerised compounds correlated with observed activities were successfully isolated. Due to the unstable nature of the isolates, further decomposition is likely contributing to the overall compound instability.
Article
Biochemical Research Methods
Kristina Kappel, Joanna Fafinska, Markus Fischer, Jan Fritsche
Summary: This study describes the development of a rapid and easy-to-use DNA microarray assay for authenticating giant tiger prawns and whiteleg shrimp. By analyzing the signal patterns of 47 crustacean specimens, the specificity of the DNA microarray for the target species was demonstrated.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Alissa Drees, Markus Fischer
Summary: The HiTS-FLIP technology improves the efficiency of aptamer selection, providing insights into the relationship between sequence, structure, and function, which supports the evolution of aptamers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Erik Schleicher, Stephan Rein, Boris Illarionov, Ariane Lehmann, Tarek Al Said, Sylwia Kacprzak, Robert Bittl, Adelbert Bacher, Markus Fischer, Stefan Weber
Summary: Flavocoenzymes are essential cofactors involved in a wide range of biological processes, with interactions with the protein environment playing a key role in their versatile biochemistry and biophysics. Studying the molecular orbital of flavins is crucial for understanding the diverse functions of the flavoprotein family, and advanced techniques such as electron paramagnetic resonance can help unravel the complex structure of flavins at a high level of resolution and accuracy.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Medicinal
Eleonora Diamanti, Mostafa M. Hamed, Antoine Lacour, Patricia Bravo, Boris Illarionov, Markus Fischer, Matthias Rottmann, Matthias Witschel, Anna K. H. Hirsch
Summary: The MEP pathway enzymes are crucial for synthesizing isoprenoids and are potential drug targets. A high-throughput screening approach led to the discovery of a novel fragment hit against PfIspD, and a systematic SAR investigation identified a new compound for structure-guided optimization. A putative binding mode for the inhibitors was proposed using a homology model of PfIspD.
Article
Biochemical Research Methods
Marina Creydt, Silke Lautner, Joerg Fromm, Markus Fischer
Summary: A non-targeted metabolomics-based approach using liquid chromatography high-resolution mass spectrometry was used to differentiate spruce wood from different geographic source areas. Despite the small distance (250 km) between the two sample sites in Germany, a distinction between the sample groups was achieved based on non-polar data sets using supervised multivariate methods. Major metabolites contributing to differentiation were identified through MS/MS experiments.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Chemistry, Analytical
Kristian von Wuthenau, Torben Segelke, Anita Kuschnereit, Markus Fischer
Summary: Counterfeiting is a widespread issue in industries like cosmetics and art, especially with expensive perfumes and valuable artworks. A study using laser ablation-inductively coupled plasma mass spectrometry successfully differentiated glass from different production sites, offering a new method for detecting counterfeits.
Article
Biochemistry & Molecular Biology
Soeren Wenck, Marina Creydt, Jule Hansen, Florian Gaerber, Markus Fischer, Stephan Seifert
Summary: This study demonstrates the importance of using random forest methods and surrogate minimal depth methods for analyzing metabolomics data. The selection of important features and evaluation of their impact on multi-level classification reveals meaningful biological relationships.
Article
Food Science & Technology
Kristian von Wuthenau, Torben Segelke, Marie-Sophie Mueller, Hardy Behlok, Markus Fischer
Summary: The study successfully used isotopolomic fingerprinting to distinguish the origin of almonds, preventing food fraud, and found that the respective harvest year and almond variety had no significant effect on origin discrimination.
Article
Food Science & Technology
David Schuetz, Janet Riedl, Elisabeth Achten, Markus Fischer
Summary: This study investigates the ability of Fourier-transform near-infrared spectroscopy to trace back the geographical origin of grain maize. Through the analysis of 101 samples from five different countries, specific spectral regions were identified as suitable for determining the origin of maize, achieving high accuracy rates.
Article
Food Science & Technology
Marina Creydt, Benjamin Wegner, Alina Gnauck, Roy Hoerner, Christian Hummert, Markus Fischer
Summary: Research efforts in the past decade have focused on developing non-targeted metabolomics strategies, especially for detecting various food authenticity parameters. This study describes the downstream process of converting a non-targeted metabolomics study into a simple targeted approach suitable for routine analysis.
Article
Chemistry, Analytical
Navid Shakiba, Annika Gerdes, Nathalie Holz, Soeren Wenck, Rene Bachmann, Tobias Schneider, Stephan Seifert, Markus Fischer, Thomas Hackl
Summary: FT-NIR spectroscopy was used to determine the geographical origin of hazelnut samples from different countries with a test accuracy of 90.6%. Data fusion of NIR and NMR data exhibited a better performance with a test accuracy of 96.6%. Comparison of outliers in all classification models revealed robust classification models were obtained.
MICROCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Henni-Karoliina Ropponen, Eleonora Diamanti, Alexandra Siemens, Boris Illarionov, Joerg Haupenthal, Markus Fischer, Matthias Rottmann, Matthias Witschel, Anna K. H. Hirsch
Summary: By repositioning an antimalarial compound class and derivatising it based on the eNTRy rules, no substantial improvement was observed against E. coli wild-type K12, but distinct activity differences were seen in mutant strains. The study highlighted that the rules for enhanced activity against Gram-negative bacteria may not always be applicable, with glycine derivatives showing the highest antibacterial activity despite efflux issues.
RSC MEDICINAL CHEMISTRY
(2021)
