Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200

Surface plasmonic biosensors: principles, designs and applications

Recently, surface plasmon resonance (SPR) biosensors have been widely used in environmental monitoring, food contamination detection and diagnosing medical conditions due to their superior sensitivity, label-free detection and rapid analysis speed. This paper briefly elaborates on the development history of SPR technology and introduces SPR signal sensing principles. A summary of recent applications of SPR sensors in different fields is highlighted, including their figures of merit and limitations. Finally, the personal perspectives and future development trends about sensor preparation and design are discussed in detail, which may be critical for improving the performance of SPR sensors.

Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening

In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) approach was developed to assess the cross-target generalization ability of machine-learning scoring functions (MLSFs). Subsequently, 12 typical MLSFs were evaluated using random cross-validation (Random-CV), protein sequence similarity-based cross-validation (Seq-CV), and pocket Pfam-based cross-validation (Pfam-CV) methods. Surprisingly, all of the tested models showed decreased performances from Random-CV to Seq-CV to Pfam-CV experiments, not showing satisfactory generalization capacity. Our interpretable analysis suggested that the predictions on novel targets by MLSFs were dependent on buried solvent-accessible surface area (SASA)-related features of complex structures, with greater predicted binding affinities on complexes owning larger protein-ligand interfaces. By combining buried SASA-related features with target-specific patterns that were only shared among structurally similar compounds in the same cluster, the random forest (RF)-Score attained a good performance in the Random-CV test. Based on these findings, we strongly advise assessing the generalization ability of MLSFs with the Pfam-cluster approach and being cautious with the features learned by MLSFs.

Easy and Rapid Approach to Obtaining the Binding Affinity of Biomolecular Interactions Based on the Deep Learning Boost

Recently, the deep learning (DL) dimension of artificial intelligence has received much attention from biochemical researchers and thus has gradually become the key approach adopted in the area of biosensing applications. Studies have shown that the use of DL techniques for sensing can not only shorten the time of data analysis but also significantly increase the accuracy of data analysis and prediction, resulting in the performance improvement of biosensing systems in comparison to conventional methods. However, obtaining reliable equilibrium and rate constants of biomolecular interactions during the detection process remains difficult and time-consuming to date. In this study, we propose a transformed model based on the deep transfer learning and sequence-to-sequence autoencoder that can successfully transfer the SPR sensorgram to the protein-binding constants, that is, the association rate constant (k_a) and dissociation rate constant (k_d), which provide crucial information to understand the mechanisms of drug action and the functional structures of biomolecules. Experimentally, we first trained and tested the pre-trained model using the Langmuir model which generated ideal SPR sensorgrams and then we fine-tuned the pre-trained model through the augmented SPR sensorgrams which were synthesized by using the synthesized minority oversampling technique (SMOTE) through the moderate-scale experiment. Next, the fine-tuned model was inputted with a short experimental SPR sensorgram that only needs 110 s, and the sensorgram was directly transformed into a reconstructed ideal sensorgram. Finally, the binding kinetic constants, that is, k_a and k_d, as outputs, were obtained through fitting the reconstructed ideal sensorgram. The results showed that the prediction errors of k_a and k_d obtained by our model were less than 12 and 24%, respectively. Based on the convenience, accuracy, and reliability of the proposed DL approach, we believe our strategy significantly boosts the feasibility to monitor the binding affinity of antibodies online during production.

Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis-Trans Isomerization and the Chameleonic Roles of Calcium

Falling outside of Lipinski's rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca²⁺, and host-guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS-MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl₃. To adopt these conformations, the macrocyclic ring has to twist and bend via cis-trans isomerization of backbone amides, and thus, we termed this family of structures the "bent" conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CD₃OD/H₂O and 55% in CD₃CN. However, upon interacting with Ca²⁺, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca²⁺ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9-MeLeu10 peptide bond into a trans bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS-MS is able to probe the solution-phase structures of the complexes and that the Ca²⁺:CycA complex may play an essential role in the binding of CycA to CypA.

Optical biosensors: an exhaustive and comprehensive review

Optical biosensors have exhibited worthwhile performance in detecting biological systems and promoting significant advances in clinical diagnostics, drug discovery, food process control, and environmental monitoring. Without complexity in their pretreatment and probable influence on the nature of target molecules, these biosensors have additional advantages such as high sensitivity, robustness, reliability, and potential to be integrated on a single chip. In this review, the state of the art optical biosensor technologies, including those based on surface plasmon resonance (SPR), optical waveguides, optical resonators, photonic crystals, and optical fibers, are presented. The principles for each type of biosensor are concisely introduced and particular emphasis has been placed on recent achievements. The strengths and weaknesses of each type of biosensor have been outlined as well. Concluding remarks regarding the perspectives of future developments are discussed.

Insights into Biophysical Methods to Study Interactions Between HIV-1 Reverse Transcriptase and Non-nucleoside Reverse Transcriptase Inhibitors

Background:

Reverse Transcriptase (RT) of immunodeficiency virus type-1 (HIV-1) remains an essential target for new antiretroviral therapies. Non-nucleoside reverse transcriptase inhibitors (or NNRTIs) constitute a major class of RT inhibitors whose characterization is essential.

Introduction:

Several biochemical, biological, and biophysical methods have been previously used to analyze the biological effects of NNRTIs. We explored here the use of surface plasmonic resonance to characterize the affinity of RT towards selected NNRTIs and compared the results with those obtained with in vitro and in cellulo assays.

Methods:

The solubility and stability in buffers of the tested NNRTIs were assessed by spectrophotometry and fluorescence. Surface plasmonic resonance experiments to study direct NNRTIs binding to immobilized RT and intramolecular quenching of RT tryptophan fluorescence were used to determine the KA association constants (= 1/KD) between RT and the inhibitors. The in vitro inhibition constants of RT were determined using kinetics and the effects on three other potential targets (proteasome, HIV-1 integrase, and HIV-1 protease) were analyzed.

Results:

The results obtained with two typical molecules belonging to our previous N-hydroxyureido acylnucleoside derivatives series using the above biophysical assays matched those obtained in in vitro and previous in cellulo assays.

Conclusion:

Surface plasmonic resonance provides reliable thermodynamic information on the interaction of RT with NNRTIs and appears as a useful method for understanding their inhibitory mechanism.

Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis

Trypanosomatids possess glycosome organelles that contain much of the glycolytic machinery, including phosphofructokinase (PFK). We present kinetic and structural data for PFK from three human pathogenic trypanosomatids, illustrating intriguing differences that may reflect evolutionary adaptations to differing ecological niches. The activity of Leishmania PFK – to a much larger extent than Trypanosoma PFK – is reliant on AMP for activity regulation, with 1 mm AMP increasing the L. infantum PFK (LiPFK) kcat/K_0.5^F6P value by 10‐fold, compared to only a 1.3‐ and 1.4‐fold increase for T. cruzi and T. brucei PFK, respectively. We also show that Leishmania PFK melts at a significantly lower (> 15 °C) temperature than Trypanosoma PFKs and that addition of either AMP or ATP results in a marked stabilization of the protein. Sequence comparisons of Trypanosoma spp. and Leishmania spp. show that divergence of the two genera involved amino acid substitutions that occur in the enzyme’s ‘reaching arms’ and ‘embracing arms’ that determine tetramer stability. The dramatic effects of AMP on Leishmania activity compared with the Trypanosoma PFKs may be explained by differences between the T‐to‐R equilibria for the two families, with the low‐melting Leishmania PFK favouring the flexible inactive T‐state in the absence of AMP. Sequence comparisons along with the enzymatic and structural data presented here also suggest there was a loss of AMP‐dependent regulation in Trypanosoma species rather than gain of this characteristic in Leishmania species and that AMP acts as a key regulator in Leishmania governing the balance between glycolysis and gluconeogenesis.

Structural and Functional Insights into Human Nuclear Cyclophilins

The peptidyl prolyl isomerases (PPI) of the cyclophilin type are distributed throughout human cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects what is known about the eight human nuclear cyclophilins: peptidyl prolyl isomerase H (PPIH), peptidyl prolyl isomerase E (PPIE), peptidyl prolyl isomerase-like 1 (PPIL1), peptidyl prolyl isomerase-like 2 (PPIL2), peptidyl prolyl isomerase-like 3 (PPIL3), peptidyl prolyl isomerase G (PPIG), spliceosome-associated protein CWC27 homolog (CWC27), and peptidyl prolyl isomerase domain and WD repeat-containing protein 1 (PPWD1). Each “spliceophilin” is evaluated in relation to the spliceosomal complex in which it has been studied, and current work studying the biological roles of these cyclophilins in the nucleus are discussed. The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, and the importance of developing spliceophilin-specific inhibitors, are considered.