Elvis A. F. Martis

Anaplastic lymphoma kinase (ALK) is a tyrosine kinase receptor implicated in cancers like breast cancer, non-small cell lung carcinoma, and neuroblastoma. Crizotinib, an ALK inhibitor, initially succeeded as a treatment for such cancers before mutations caused its failure. We investigated the mechanism of resistance due to mutations like C1156Y, L1196M, G1269A, L1198F, and C1156Y/L1198F through validated computational methods and published experimental data. Our analysis reveals that these mutations do not reduce the binding affinity or alter the binding conformation of crizotinib, consistent with published X-ray crystallographic and biochemical data. This study is the first to show the conformational change in ALK's activation loop (\textbf{A-loop}) due to phosphorylation, as there is no experimental structure for phosphorylated ALK. Principal component analysis confirms that A-loop dynamics is primarily responsible for ALK activation, explaining the changes in catalytic efficiency due to phosphorylation or mutants like C1156Y and L1198F. Our results conclusively demonstrate that mutations like C1156Y influence A-loop dynamics, leading to an ATP-independent activation. Therefore, ATP competitive inhibitors like crizotinib will inevitably lose their therapeutic effectiveness without losing their binding affinity to ALK.

Molecular docking is a useful method for predicting the binding affinity and conformation of small chemical entities to support lead optimisation. It is also used to virtually screen a large chemical database to find new chemical entities. There are several docking programs available with different algorithms and varying preparation steps. We identify ten quick tips that apply to molecular docking irrespective of the program one might choose. Our objective is to provide the beginners with important things to keep in mind while using molecular docking for their research. We aim to ensure that experts and beginners can perform molecular docking to yield biologically relevant and reproducible results.

Cilia are microtubule‐based sensory organelles present in a number of eukaryotic cells. Mutations in the genes encoding ciliary proteins cause ciliopathies in humans. A‐kinase anchoring proteins (AKAPs) tether ciliary signaling proteins such as protein kinase A (PKA). The dimerization and docking domain (D/D) on the RIIα subunit of PKA interacts with AKAPs. Here, we show that AKAP240 from the central‐pair microtubules of Chlamydomonas reinhardtii cilia uses two C‐terminal amphipathic helices to bind to its partner FAP174, an RIIα‐like protein with a D/D domain at the N‐terminus. Co‐immunoprecipitation using anti‐FAP174 antibody with an enriched central‐pair microtubule fraction isolated seven interactors whose mass spectrometry analysis revealed proteins from the C2a (FAP65, FAP70, and FAP147) and C1b (CPC1, HSP70A, and FAP42) microtubule projections and FAP75, a protein whose sub‐ciliary localization is unknown. Using RII D/D and FAP174 as baits, we identified two additional AKAPs (CPC1 and FAP297) in the central‐pair microtubules.

Withdrawal Statement: The authors have withdrawn this manuscript because the reviewers have suggested significant revision of the manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

A new, cost-effective and fast chromatographic method using sulfated β-cyclodextrin (SβCD) as a chiral mobile phase additive (CMPA) was developed and validated for the enantiomeric separation of milnacipran. Milnacipran is an anti-depressant drug. Levo-milnacipran is the active enantiomer with less adverse effects than dextro-milnacipran. Hence, it is imperative to separate the enantiomers of milnacipran. Various parameters affecting enantiomeric resolution, for instance, the effect of type and concentration of cyclodextrins, the effect of pH of the mobile phase, effect of type and concentration of the organic solvent in the mobile phase and effect of type of achiral column, were investigated. We demonstrated successful resolution of enantiomers of milnacipran on reverse-phase HPLC with Kinetex C8 column (150x4.6mm, 5µ), using a mobile phase consisting of 18:82 v/v acetonitrile: 10mM sodium dihydrogen orthophosphate dihydrate buffer pH 3.0 (adjusted with orthophosphoric acid) containing 10mM SβCD with a flow rate 1.0 ml/minute. The column temperature was ambient and UV detection was carried out at 227 nm with an injection volume of 20µl. This method for enantiomeric separation of milnacipran was validated in accordance with ICH guidelines and successfully applied to the marketed formulation of Levomilnacipran. Furthermore, molecular docking was used to identify the chiral recognition mechanism. The results of molecular docking corroborated with our experimental findings.

A new, cost-effective and fast chromatographic method using sulfated β-cyclodextrin (SβCD) as a chiral mobile phase additive (CMPA) was developed and validated for the enantiomeric separation of milnacipran. Milnacipran is an anti-depressant drug. Levo-milnacipran is the active enantiomer with less adverse effects than dextro-milnacipran. Hence, it is imperative to separate the enantiomers of milnacipran. Various parameters affecting enantiomeric resolution, for instance, the effect of type and concentration of cyclodextrins, the effect of pH of the mobile phase, effect of type and concentration of the organic solvent in the mobile phase and effect of type of achiral column, were investigated. We demonstrated successful resolution of enantiomers of milnacipran on reverse-phase HPLC with Kinetex C8 column (150x4.6mm, 5µ), using a mobile phase consisting of 18:82 v/v acetonitrile: 10mM sodium dihydrogen orthophosphate dihydrate buffer pH 3.0 (adjusted with orthophosphoric acid) containing 10mM SβCD with a flow rate 1.0 ml/minute. The column temperature was ambient and UV detection was carried out at 227 nm with an injection volume of 20µl. This method for enantiomeric separation of milnacipran was validated in accordance with ICH guidelines and successfully applied to the marketed formulation of Levomilnacipran. Furthermore, molecular docking was used to identify the chiral recognition mechanism. The results of molecular docking corroborated with our experimental findings. A new, cost-effective and fast chromatographic method using sulfated β-cyclodextrin (SβCD) as a chiral mobile phase additive (CMPA) was developed and validated for the enantiomeric separation of milnacipran. Milnacipran is an anti-depressant drug. Levo-milnacipran is the active enantiomer with less adverse effects than dextro-milnacipran. Hence, it is imperative to separate the enantiomers of milnacipran. Various parameters affecting enantiomeric resolution, for instance, the effect of type and concentration of cyclodextrins, the effect of pH of the mobile phase, effect of type and concentration of the organic solvent in the mobile phase and effect of type of achiral column, were investigated. We demonstrated successful resolution of enantiomers of milnacipran on reverse-phase HPLC with Kinetex C8 column (150x4.6mm, 5µ), using a mobile phase consisting of 18:82 v/v acetonitrile: 10mM sodium dihydrogen orthophosphate dihydrate buffer pH 3.0 (adjusted with orthophosphoric acid) containing 10mM SβCD with a flow rate 1.0 ml/minute. The column temperature was ambient and UV detection was carried out at 227 nm with an injection volume of 20µl. This method for enantiomeric separation of milnacipran was validated in accordance with ICH guidelines and successfully applied to the marketed formulation of Levomilnacipran. Furthermore, molecular docking was used to identify the chiral recognition mechanism. The results of molecular docking corroborated with our experimental findings.

Drug discovery is a continuously evolving area, essential for mankind albeit a very expensive process with a high attrition rate. The main challenge faced by pharmaceutical researchers today is to identify the major hurdles and validate the “developability” of a compound in the initial stages of drug development in order to select superior drug candidates with the best chances of success. This motivated us to introduce a “universal” approach for analyzing the pharmacodynamics, pharmacokinetics and toxicity profile of compounds based on the philosophy of QSAR. The present work deals with the development, validation and application of a novel QSPR formalism entitled EigenValue ANalySis (EVANS). This methodology encodes 3D structural information in terms of the atom pair distances along with molecular physicochemical properties to generate a set of unique hybrid descriptors, termed as “Eigenvalues.” The present article deals with the intricacies of the methodology and explores its applicability on a series of datasets for building pharmacodynamic QSAR models.