Drug design in the exascale era: a perspective from massively parallel QM/MM simulations

B Raghavan, M Paulikat, K Ahmad… - Journal of chemical …, 2023 - ACS Publications
The initial phases of drug discovery–in silico drug design–could benefit from first principle
Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations …

Cadherin profiling for therapeutic interventions in Epithelial Mesenchymal Transition (EMT) and tumorigenesis

M Pal, S Bhattacharya, G Kalyan, S Hazra - Experimental cell research, 2018 - Elsevier
The major hallmarks of Epithelial-Mesenchymal Transition (EMT) is the loss of epithelial cell
polarity and loss of expression of the cell-cell adhesion molecule like E-cadherin and …

Nano‐and Microscale Confinements in DNA‐Scaffolded Enzyme Cascade Reactions

S Kröll, T Burgahn, KS Rabe, M Franzreb… - Small, 2024 - Wiley Online Library
Artificial reconstruction of naturally evolved principles, such as compartmentalization and
cascading of multienzyme complexes, offers enormous potential for the development of …

Recent advances in light-driven C–H bond activation and building C–C bonds with CO 2 as a feedstock for carbon capture and utilization technology

T Katagiri, Y Amao - Green Chemistry, 2020 - pubs.rsc.org
CO2 is a representative greenhouse gas (GHG), and the Paris Agreement adopted by
consensus on 12 December 2015 mandates worldwide reduction of CO2 emissions by 80 …

Low birth weight influences the postnatal abundance and characteristics of satellite cell subpopulations in pigs

K Stange, C Miersch, G Sponder, M Röntgen - Scientific reports, 2020 - nature.com
Low birth weight (LBW) can cause lifelong impairments in muscle development and growth.
Satellite cells (SC) and their progeny are crucial contributors to myogenic processes. This …

Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes

PF Fitzpatrick - Biochimica et Biophysica Acta (BBA)-Proteins and …, 2015 - Elsevier
Oxidation of alcohols and amines is catalyzed by multiple families of flavin-and pyridine
nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique …

Metabolomics of Central Carbon Metabolism in Mycobacterium tuberculosis

AD Baughn, KY Rhee - Molecular Genetics of Mycobacteria, 2014 - Wiley Online Library
Central carbon metabolism (CCM)—defined as the enzymatic transformation of carbon
through glycolysis, the pentose phosphate pathway (PPP), the citric acid cycle, the …

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria

P Murima, M Zimmermann, T Chopra, F Pojer… - Nature …, 2016 - nature.com
Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium
tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux …

Elucidating the antimycobacterial mechanism of action of decoquinate derivative RMB041 using metabolomics

KE Knoll, Z Lindeque, AA Adeniji, CB Oosthuizen… - Antibiotics, 2021 - mdpi.com
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still remains one of the
leading causes of death from a single infectious agent worldwide. The high prevalence of …

Novel Type II and Monomeric NAD+ Specific Isocitrate Dehydrogenases: Phylogenetic Affinity, Enzymatic Characterization and Evolutionary Implication

P Wang, C Lv, G Zhu - Scientific reports, 2015 - nature.com
NAD+ use is an ancestral trait of isocitrate dehydrogenase (IDH) and the NADP+ phenotype
arose through evolution as an ancient adaptation event. However, no NAD+-specific IDHs …