In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study

Computation-guided transcription factor biosensor specificity engineering for adipic acid detection

Transcription factor (TF)-based biosensors that connect small-molecule sensing with readouts such as fluorescence have proven to be useful synthetic biology tools for applications in biotechnology. However, the development of specific TF-based biosensors is hindered by the limited repertoire of TFs specific for molecules of interest since current construction methods rely on a limited set of characterized TFs. In this study, we present an approach for engineering the specificity of TFs through a computation-based workflow using molecular docking that enables targeted alteration of TF ligand specificity. Using this method, we engineer the LysR family BenM TF to alter its specificity from its cognate ligand cis,cis-muconic acid to adipic acid through a single amino acid substitution identified by our computational workflow. When implemented in a cell-free system, the engineered biosensor shows higher ligand sensitivity, expanding the potential applications of this circuit. We further investigate ligand binding through molecular dynamics to analyze the substitution, elucidating the impact of modulating a single amino acid position on the mechanism of BenM ligand binding. This study represents the first application of biomolecular modeling methods for altering BenM specificity and for gaining insights into how mutations influence the structural dynamics of BenM. Such methods can potentially be applied to other TFs to alter specificity and analyze the dynamics responsible for these changes, highlighting the applicability of computational tools for informing experiments. In addition, our developed adipic acid biosensor can be applied for the identification and engineering of enzymes to produce adipic acid.

From in-silico screening to in-vitro evaluation: Enhancing the detection of Microcystins with engineered PP1 mutant variants

Cyanotoxins produced during harmful algal blooms (CyanoHABs) have become a worldwide issue of concern. Microcystins (MC) are the most ubiquitous group of cyanotoxins and have known carcinogenic and hepatotoxic effects. The protein phosphatase inhibition assays (PPIAs), based on the inhibition of Protein Phosphatase 1/2A (PP1/PP2A) by MC, are one of the most cost-effective options for detecting MC. In this work, we aimed to design in-silico and evaluate in-vitro mutant variants of the PP1 protein, in order to enhance their capabilities as a MC biosensor. To this end, we performed an in-silico active site-saturated mutagenesis screening, followed by stability and docking affinity calculation with the MCLR cyanotoxin. Candidates with improved both affinity and stability were further tested in a fully flexible active-site docking. The best-scored mutations (19) were individually analysed regarding their locations and interactions. Four of them (p.D197F; p.Q249Y; p.S129W; p.D220Q) were selected for in-vitro expression and evaluation. Mutant p.D197F, exhibited a significant increment in inhibition by MCLR with respect to the WT, while showing a non-significant difference in stability nor activity. This successful PP1 inhibition enhancement suggests the potential of the p.D197F variant for practical MC detection applications.

Bioinformatics insights into CENP-T and CENP-W protein-protein interaction disruptive amino acid substitution in the CENP-T-W complex

Kinetochores are multi-protein assemblies present at the centromere of the human chromosome and play a crucial role in cellular mitosis. The CENP-T and CENP-W chains form a heterodimer, which is an integral part of the inner kinetochore, interacting with the linker DNA on one side and the outer kinetochore on the other. Additionally, the CENP-T-W dimer interacts with other regulatory proteins involved in forming inner kinetochores. The specific roles of different amino acids in the CENP-W at the protein-protein interaction (PPI) interface during the CENP-T-W dimer formation remain incompletely understood. Since cell division goes awry in diseases like cancer, this CENP-T-W partnership is a potential target for new drugs that could restore healthy cell division. We employed molecular docking, binding free energy calculations, and molecular dynamics (MD) simulations to investigate the disruptive effects of amino acids substitutions in the CENP-W chain on CENP-T-W dimer formation. By conducting a molecular docking study and analysing hydrogen bonding interactions, we identified key residues in CENP-W (ASN-46, ARG-53, LEU-83, SER-86, ARG-87, and GLY-88) for further investigation. Through site-directed mutagenesis and subsequent binding free energy calculations, we refined the selection of mutant. We chose four mutants (N46K, R53K, L83K, and R87E) of CENP-W to assess their comparative potential in forming CENP-T-W dimer. Our analysis from 250 ns long revealed that the substitution of LEU83 and ARG53 residues in CENP-W with the LYS significantly disrupts the formation of CENP-T-W dimer. In conclusion, LEU83 and ARG53 play a critical role in CENP-T and CENP-W dimerization which is ultimately required for cellular mitosis. Our findings not only deepen our understanding of cell division but also hint at exciting drug-target possibilities.

Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression

The cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.

Modification of an Anopheles gambiae odorant binding protein to create an array of chemical sensors for detection of drugs

The binding pockets of odorant binding proteins from Anopheles gambiae (OBP1 and OBP47) were analysed using in silico modelling. The feasibility of creating mutant proteins to achieve a protein array capable of detecting drugs of abuse in solution or in vapour phase was investigated. OBP1 was found to be easily adapted and several mutant proteins were expressed and characterised. AgamOBP1_S82P was found to have high affinities to cannabinol, 3,4-methylenedioxy methamphetamine (MDMA/Ecstasy) and cocaine hydrochloride. When these proteins were immobilised on a quartz crystal microbalance, saturated cocaine hydrochloride vapour could be detected. The sensors were stable over a period of at least 10 months in air. The approach taken allows flexible design of new biosensors based on inherently stable protein scaffolds taking advantage of the tertiary structure of odorant binding proteins.

Advances in distributed computing with modern drug discovery

INTRODUCTION

Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms. Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD). Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.

Phosphatidylcholine in the groove of endothelial cell protein C receptor (EPCR) regulates EPCR conformation and protein C recognition

Endothelial cell protein C receptor (EPCR), the cellular receptor for protein C (PC), facilitates PC activation through the thrombin/thrombomodulin complex and regulates thrombin generation. Under pathophysiological conditions like sepsis, the interactions between EPCR and PC become impaired. Previous studies have demonstrated that the EPCR contains a phospholipid in the antigen-binding groove that is responsible for the structural stability of the EPCR and for PC recognition. However, an understanding at the atomic level during ligand recognition is not fully developed. Molecular dynamics simulations along with potential of mean force (PMF) calculations were carried out in order to provide molecular insight into the dynamics and free energies of EPCR-PC in the absence/presence of phospholipid, namely lysophosphatidylcholine (lysoPCh) and phosphatidylcholine (PCh) in the antigen-binding groove of the EPCR. Our data reveal that the presence of lipid maintains the optimal conformation of the EPCR for PC binding. PMF data further suggest that the PCh system is the most stable in comparison with the other systems (lysoPCh and no lipid). With regards to the two hydrophobic tails of PCh, one lipid tail regulates EPCR conformation while the other promotes ligand recognition by interacting with the keel residue (Phe-4) of PC. Due to the lack of one hydrophobic tail for the lysoPCh system, the EPCR conformation is retained but the affinity of the EPCR towards the ligand (PC) is reduced. Our studies for the first time explore the possible mode of ligand recognition by the EPCR via the involvement of phosphatidylcholine within its hydrophobic groove. The present work provides insight into PCh-dependent ligand recognition and hence regulation of the protein C/EPCR complex formation.

Investigation of binding behaviour of procainamide hydrochloride with human serum albumin using synchronous, 3D fluorescence and circular dichroism

Interaction of procainamide hydrochloride (PAH) with human serum albumin (HSA) is of great significance in understanding the pharmacokinetic and pharmacodynamic mechanisms of the drug. Multi-spectroscopic techniques were used to investigate the binding mode of PAH to HSA and results revealed the presence of static type of quenching mechanism. The number of binding sites, binding constants and thermodynamic parameters were calculated. The results showed a spontaneous binding of PAH to HSA and hydrophobic interactions played a major role. In addition, the distance between PAH and the Trp-214 was estimated employing the Förster's theory. Site marker competitive experiments indicated that the binding of PAH to HSA primarily took place in subdomain IIA (Sudlow's site I). The influence of interference of some common metal ions on the binding of PAH to HSA was studied. Synchronous fluorescence spectra (SFS), 3D fluorescence spectra and circular dichroism (CD) results indicated the conformational changes in the structure of HSA.

Predicting the impact of mutations on the specific activity of Bacillus thermocatenulatus lipase using a combined approach of docking and molecular dynamics

Lipases are important biocatalysts owing to their ability to catalyze diverse reactions with exceptional substrate specificities. A combined docking and molecular dynamics (MD) approach was applied to study the chain-length selectivity of Bacillus thermocatenulatus lipase (BTL2) towards its natural substrates (triacylglycerols). A scoring function including electrostatic, van der Waals (vdW) and desolvation energies along with conformational entropy was developed to predict the impact of mutation. The native BTL2 and its 6 mutants (F17A, V175A, V175F, D176F, T178V and I320F) were experimentally analyzed to determine their specific activities towards tributyrin (C4) or tricaprylin (C8), which were used to test our approach. Our scoring methodology predicted the chain-length selectivity of BTL2 with 85.7% (6/7) accuracy with a positive correlation between the calculated scores and the experimental activity values (r = 0.82, p = 0.0004). Additionally, the impact of mutation on activity was predicted with 75% (9/12) accuracy. The described study represents a fast and reliable approach to accurately predict the effect of mutations on the activity and selectivity of lipases and also of other enzymes. Copyright © 2016 John Wiley & Sons, Ltd.

Exploring the role of the phospholipid ligand in endothelial protein C receptor: a molecular dynamics study

Endothelial protein C receptor (EPCR) is a CD1-like transmembrane glycoprotein with important regulatory roles in protein C (PC) pathway, enhancing PC's anticoagulant, anti-inflammatory, and antiapoptotic activities. Similarly to homologous CD1d, EPCR binds a phospholipid [phosphatidylethanolamine (PTY)] in a groove corresponding to the antigen-presenting site, although it is not clear if lipid exchange can occur in EPCR as in CD1d. The presence of PTY seems essential for PC gamma-carboxyglutamic acid (Gla) domain binding. However, the lipid-free form of the EPCR has not been characterized. We have investigated the structural role of PTY on EPCR, by multiple molecular dynamics (MD) simulations of ligand bound and unbound forms of the protein. Structural changes, subsequent to ligand removal, led to identification of two stable and folded ligand-free conformations. Compared with the bound form, unbound structures showed a narrowing of the A' pocket and a high flexibility of the helices around it, in agreement with CD1d simulation. Thus, a lipid exchange with a mechanism similar to CD1d is proposed. In addition, unbound conformations presented a reduced interaction surface for Gla domain, confirming the role of PTY in establishing the proper EPCR conformation for the interaction with its partner protein. Single MD simulations were also obtained for 29 mutant models with predicted structural stability and impaired binding ability. Ligand affinity calculations, based on linear interaction energy method, showed that substitution-induced conformational changes affecting helices around the A' pocket were associated to a reduced binding affinity. Mutants responsible for this effect may represent useful reagents for experimental tests.