Review
Microbiology
Constanze Kuhlisch, Adva Shemi, Noa Barak-Gavish, Daniella Schatz, Assaf Vardi
Summary: The cycling of major nutrients in the ocean is influenced by large-scale phytoplankton blooms, which are hot spots of microbial life. Microbial interactions, mediated by chemical crosstalk, play a crucial role in determining the type and outcome of these interactions. These interactions between microorganisms and algae are dependent on the environmental context.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Anthony C. Yu, Huada Lian, Xian Kong, Hector Lopez Hernandez, Jian Qin, Eric A. Appel
Summary: Studies suggest that entropy-driven physical networks exhibit invariant mechanical properties at elevated temperatures, in contrast to enthalpy-dominated crosslinking networks. By connecting thermodynamics and temperature-dependent viscoelasticity in a mathematical framework, the temperature dependence of crosslinking interactions is explored.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Sara Seweryn, Katarzyna Skirlinska-Nosek, Natalia Wilkosz, Kamila Sofinska, David Perez-Guaita, Magdalena Ocwieja, Jakub Barbasz, Marek Szymonski, Ewelina Lipiec
Summary: This study investigated the repair process of DNA double-strand breaks (DSBs) induced by the anticancer antibiotic bleomycin (BLM) using a multimodal approach. By analyzing the SERS results, spectral bands associated with DSBs were identified, indicating conformational modifications and strand ruptures. A model was established to predict the number of DSBs and detect spectroscopic markers of DNA damage and conformational changes.
SCIENTIFIC REPORTS
(2022)
Article
Spectroscopy
Yugao Xu, Tingting Yang, Tao Lu, Gang Feng
Summary: The conformational equilibria of cyclohexyl isothiocyanate and its complex with water were investigated by microwave spectroscopy and theoretical calculations. The rotational spectra of the two conformers of the bare cyclohexyl isothiocyanate, a-trans and e-trans, were measured and analyzed, as well as their isotopologues. For the binary complex with water, the rotational spectra of the monohydrates of both a-trans and e-trans were measured, and water isotopologues were also observed. The noncovalent bonding features of the monohydrates were examined using natural bond orbital analysis and symmetry-adapted perturbation theory analysis.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Crystallography
Katherine Standish, Matthias Zeller, Antonio J. Barbosa, Patrick C. Hillesheim
Summary: This study examines two polymorphs of a benzoxadiazole derivative to determine the interactions leading to the formation of distinct crystalline forms. The findings highlight the crucial role of pi interactions and carbonyl interactions in the crystal structure formation.
Article
Chemistry, Physical
Pancham Lal Gupta, Heather A. Carlson
Summary: In drug design, molecular dynamics calculations of protein-fragment pairs can determine the nearest hot spots, guiding the direction and type of chemical modifications that can improve binding affinity. This method provides a general framework for choosing chemical groups to grow lead molecules and improve drug design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Chenghui Shi, Julia Kaffy, Tap Ha-Duong, Jean-Francois Gallard, Alain Pruvost, Aloise Mabondzo, Lidia Ciccone, Sandrine Ongeri, Nicolo Tonali
Summary: A novel class of peptidomimetic foldamers based on diaza-peptide units is reported, which can undergo helical folding in water and have potential applications in protein-protein interaction and amyloid protein aggregation.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Yanqing Yang, Joseph Cheramy, Yunjie Xu
Summary: The conformational landscape and aggregation behavior of THFA were investigated using MI-VCD, revealing unusual structures formed in a cold rare gas matrix. Experiment results showed the presence of trans and cis conformers of THFA, as well as the formation of a few hundred stable binary conformers. This study highlights the power of MI-VCD spectroscopy in identifying unique structures in a controlled environment.
Article
Chemistry, Multidisciplinary
Jennifer Gilbert, Inna Ermilova, Marco Fornasier, Maximilian Skoda, Giovanna Fragneto, Jan Swenson, Tommy Nylander
Summary: The interaction between cationic ionisable lipids (CIL) and nucleic acids (NAs) is influenced by pH and NA type, which affects the adsorption behavior and structure of the lipid layer. It is also found that the secondary structure of NAs has an impact on the interaction.
Article
Biochemistry & Molecular Biology
Rebecca L. L. Whitehouse, Wesam S. S. Alwan, Olga V. V. Ilyichova, Ashley J. J. Taylor, Indu R. R. Chandrashekaran, Biswaranjan Mohanty, Bradley C. C. Doak, Martin J. J. Scanlon
Summary: Fragment-based drug design relies on structural information obtained through X-ray crystallography to evolve fragments into lead-like compounds through structure-based design. The composition of compound libraries can be optimized to probe binding hot spots on protein surfaces.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Lu Sun, Hongjun Fan, Shijun Zhong
Summary: Carbapenems act as irreversible covalent binders and slow substrates to the class A beta-lactamase of Mycobacterium tuberculosis, inhibiting its hydrolysis of beta-lactam drugs. Noncovalent interactions were found to dominate the binding difference for carbapenems, leading to the identification of new tight-binding carbapenems through a computational protocol.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Microbiology
Vipin Gupta, Shazia Haider, Mansi Verma, Nirjara Singhvi, Kalaisaran Ponnusamy, Md. Zubbair Malik, Helianthous Verma, Roshan Kumar, Utkarsh Sood, Princy Hira, Shiva Satija, Yogendra Singh, Rup Lal
Summary: The study provides insights into the population-specific variations attributing to the high rate of SARS-CoV-2 infections in specific geographical regions, particularly in the United States. It identifies key mutations and co-mutations in the virus genomes and suggests potential therapeutic targets for COVID-19 treatment. Additionally, the analysis of host-pathogen interactions and CpG islands sheds light on the pathogenesis of the disease, emphasizing the importance of understanding the geographical distribution of genetic variations in combatting the pandemic.
Article
Biochemistry & Molecular Biology
Dmitry E. Petrenko, David M. Karlinsky, Veronika D. Gordeeva, Georgij P. Arapidi, Elena V. Britikova, Vladimir V. Britikov, Alena Y. Nikolaeva, Konstantin M. Boyko, Vladimir I. Timofeev, Inna P. Kuranova, Anna G. Mikhailova, Eduard V. Bocharov, Tatiana V. Rakitina
Summary: The crystal structure of bacterial oligopeptidase B from Serratia proteamaculans in complex with a chloromethyl ketone inhibitor was determined, revealing a closed conformation in the active state. The structure showed that a single inhibitor molecule binds to the catalytic residues S532 and H652, mimicking a tetrahedral intermediate. Comparative analysis with a similar enzyme from Trypanosoma brucei revealed different interdomain interactions in bacterial OpBs, with a complementary oppositely charged surface in SpOpB instead of a salt bridge in TbOpB. Bioinformatics analysis and structural modeling classified bacterial OpBs into two groups based on the modes of D-loop stabilization in closed conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Medicinal
Bin Zhao, Ajaybabu. V. V. Pobbati, Brian. P. P. Rubin, Shaun Stauffer
Summary: The Hippo signaling pathway is involved in cell proliferation and apoptosis, and the YAP/TAZ-TEAD interaction is an important target for cancer treatment. Direct small molecule disruptors targeting TEAD interfaces 2 and 3 pose challenges in inhibitor development.
Article
Chemistry, Medicinal
Adela Jilkova, Petra Rubesova, Jindrich Fanfrlik, Pavla Fajtova, Pavlina Rezacova, Jiri Brynda, Martin Lepsik, Helena Mertlikova-Kaiserova, Cory D. Emal, Adam R. Renslo, William R. Roush, Martin Horn, Conor R. Caffrey, Michael Mares
Summary: This study identified potent inhibitors of Schistosoma mansoni cathepsin B1, a validated drug target for schistosomiasis treatment. The inhibitors showed high bioactivity against the pathogen, selectivity for the target enzyme, and favorable metabolic stability. These results provide structural insights for the rational design of next-generation inhibitors for potential schistosomiasis drugs.
ACS INFECTIOUS DISEASES
(2021)
Article
Biochemical Research Methods
Preethi Badrinarayan, G. Narahari Sastry
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2011)
Article
Pharmacology & Pharmacy
Preethi Badrinarayan, G. Narahari Sastry
CURRENT PHARMACEUTICAL DESIGN
(2013)
Article
Chemistry, Medicinal
Preethi Badrinarayan, G. Narahari Sastry
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2011)
Article
Biochemical Research Methods
Preethi Badrinarayan, G. Narahari Sastry
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2012)
Article
Biochemistry & Molecular Biology
Preethi Badrinarayan, P. Srivani, G. Narahari Sastry
JOURNAL OF MOLECULAR MODELING
(2011)
Article
Chemistry, Medicinal
R. Ranga Rao, Ashok K. Tiwari, P. Prabhakar Reddy, K. Suresh Babu, G. Suresh, A. Zehra Ali, K. Madhusudana, Sachin B. Agawane, Preethi Badrinarayan, G. Narahari Sastry, J. Madhusudana Rao
MEDICINAL CHEMISTRY RESEARCH
(2012)
Article
Biochemistry & Molecular Biology
Jyotsana Singh, Ritesh Singh, Preeti Gupta, Smita Rai, Asha Ganesher, Preethi Badrinarayan, G. Narahari Sastry, Rituraj Konwar, Gautam Panda
BIOORGANIC & MEDICINAL CHEMISTRY
(2017)