FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures

Protein mapping distributes many copies of different molecular probes on the surface of a target protein in order to determine binding hot spots, regions that are highly preferable for ligand binding. While mapping of X-ray structures by the FTMap server is inherently static, this limitation can be overcome by the simultaneous analysis of multiple structures of the protein. FTMove is an automated web server that implements this approach. From the input of a target protein, by PDB code, the server identifies all structures of the protein available in the PDB, runs mapping on them, and combines the results to form binding hot spots and binding sites. The user may also upload their own protein structures, bypassing the PDB search for similar structures. Output of the server consists of the consensus binding sites and the individual mapping results for each structure - including the number of probes located in each binding site, for each structure. This level of detail allows the users to investigate how the strength of a binding site relates to the protein conformation, other binding sites, and the presence of ligands or mutations. In addition, the structures are clustered on the basis of their binding properties. The use of FTMove is demonstrated by application to 22 proteins with known allosteric binding sites; the orthosteric and allosteric binding sites were identified in all but one case, and the sites were typically ranked among the top five. The FTMove server is publicly available at https://ftmove.bu.edu.

Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap

Starting with a crystal structure of a macromolecule, computational structural modeling can help to understand the associated biological processes, structure and function, as well as to reduce the number of further experiments required to characterize a given molecular entity. In the past decade, two classes of powerful automated tools for investigating the binding properties of proteins have been developed: the protein–protein docking program ClusPro and the FTMap and FTSite programs for protein hotspot identification. These methods have been widely used by the research community by means of publicly available online servers, and models built using these automated tools have been reported in a large number of publications. Importantly, additional experimental information can be leveraged to further improve the predictive power of these approaches. Here, an overview of the methods and their biological applications is provided together with a brief interpretation of the results.

Assessing the binding properties of CASP14 targets and models

An important question is how well the models submitted to CASP retain the properties of target structures. We investigate several properties related to binding. First we explore the binding of small molecules as probes, and count the number of interactions between each residue and such probes, resulting in a binding fingerprint. The similarity between two fingerprints, one for the X-ray structure and the other for a model, is determined by calculating their correlation coefficient. The fingerprint similarity weakly correlates with global measures of accuracy, and GDT_TS higher than 80 is a necessary but not sufficient condition for the conservation of surface binding properties. The advantage of this approach is that it can be carried out without information on potential ligands and their binding sites. The latter information was available for a few targets, and we explored whether the CASP14 models can be used to predict binding sites and to dock small ligands. Finally, we tested the ability of models to reproduce protein-protein interactions by docking both the X-ray structures and the models to their interaction partners in complexes. The analysis showed that in CASP14 the quality of individual domain models is approaching that offered by X-ray crystallography, and hence such models can be successfully used for the identification of binding and regulatory sites, as well as for assembling obligatory protein-protein complexes. Success of ligand docking, however, often depends on fine details of the binding interface, and thus may require accounting for conformational changes by simulation methods.

Conservation of binding properties in protein models

We study the models submitted to round 12 of the Critical Assessment of protein Structure Prediction (CASP) experiment to assess how well the binding properties are conserved when the X-ray structures of the target proteins are replaced by their models. To explore small molecule binding we generate distributions of molecular probes - which are fragment-sized organic molecules of varying size, shape, and polarity - around the protein, and count the number of interactions between each residue and the probes, resulting in a vector of interactions we call a binding fingerprint. The similarity between two fingerprints, one for the X-ray structure and the other for a model of the protein, is determined by calculating the correlation coefficient between the two vectors. The resulting correlation coefficients are shown to correlate with global measures of accuracy established in CASP, and the relationship yields an accuracy threshold that has to be reached for meaningful binding surface conservation. The clusters formed by the probe molecules reliably predict binding hot spots and ligand binding sites in both X-ray structures and reasonably accurate models of the target, but ensembles of models may be needed for assessing the availability of proper binding pockets. We explored ligand docking to the few targets that had bound ligands in the X-ray structure. More targets were available to assess the ability of the models to reproduce protein-protein interactions by docking both the X-ray structures and models to their interaction partners in complexes. It was shown that this application is more difficult than finding small ligand binding sites, and the success rates heavily depend on the local structure in the potential interface. In particular, predicted conformations of flexible loops are frequently incorrect in otherwise highly accurate models, and may prevent predicting correct protein-protein interactions.

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site. Only two of these are exploited by Nrf2, which alanine scanning of both proteins shows to bind primarily through E79 and E82 interacting with KEAP1 residues S363, R380, R415, R483, and S508. We identify fragment hits and obtain X-ray complex structures for three fragments via crystal soaking using a new crystal form of KEAP1. Combining these results provides a comprehensive and quantitative picture of the origins of binding energy at the interface. Our findings additionally reveal non-native interactions that might be exploited in the design of uncharged synthetic ligands to occupy the same site on KEAP1 that has evolved to bind the highly charged DEETGE binding loop of Nrf2. These include π-stacking with KEAP1 Y525 and interactions at an FTMap-identified hot spot deep in the binding site. Finally, we discuss how the complementary information provided by alanine-scanning mutagenesis, fragment screening, and computational hot spot mapping can be integrated to more comprehensively evaluate PPI druggability.

ClusPro LigTBM: Automated Template-based Small Molecule Docking

The template-based approach has been essential for achieving high-quality models in the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predicted Interactions). However, few such automated methods exist for protein-small molecule docking. In this paper, we present an algorithm for template-based docking of small molecules. It searches for known complexes with ligands that have partial coverage of the target ligand, performs conformational sampling and template-guided energy refinement to produce a variety of possible poses, and then scores the refined poses. The algorithm is available as the automated ClusPro LigTBM server. It allows the user to specify the target protein as a PDB file and the ligand as a SMILES string. The server then searches for templates and uses them for docking, presenting the user with top-scoring poses and their confidence scores. The method is tested on the Astex Diverse benchmark, as well as on the targets from the last round of the D3R (Drug Design Data Resource) Grand Challenge. The server is publicly available as part of the ClusPro docking server suite at https://ligtbm.cluspro.org/.

Why Some Targets Benefit from beyond Rule of Five Drugs

Beyond rule-of-five (bRo5) compounds are increasingly used in drug discovery. Here we analyze 37 target proteins that have bRo5 drugs or clinical candidates. Targets can benefit from bRo5 drugs if they have "complex" hot spot structure with four or more hots spots, including some strong ones. Complex I targets show positive correlation between binding affinity and molecular weight. These targets are conventionally druggable, but reaching additional hot spots enables improved pharmaceutical properties. Complex II targets, mostly protein kinases, also have strong hot spots but show no correlation between affinity and ligand molecular weight, and the primary motivation for creating larger drugs is to increase selectivity. Each target considered as complex III has some specific reason for requiring bRo5 drugs. Finally, targets with "simple" hot spot structure, i.e., three or fewer weak hot spots, must use larger compounds that interact with surfaces beyond the hot spot region to achieve acceptable affinity.

Cryptic binding sites on proteins: definition, detection, and druggability

Many proteins in their unbound structures lack surface pockets appropriately sized for drug binding. Hence, a variety of experimental and computational tools have been developed for the identification of cryptic sites that are not evident in the unbound protein but form upon ligand binding, and can provide tractable drug target sites. The goal of this review is to discuss the definition, detection, and druggability of such sites, and their potential value for drug discovery. Novel methods based on molecular dynamics simulations are particularly promising and yield a large number of transient pockets, but it has been shown that only a minority of such sites are generally capable of binding ligands with substantial affinity. Based on recent studies, current methodology can be improved by combining molecular dynamics with fragment docking and machine learning approaches.

Inferring Intracellular Signal Transduction Circuitry from Molecular Perturbation Experiments

The development of network inference methodologies that accurately predict connectivity in dysregulated pathways may enable the rational selection of patient therapies. Accurately inferring an intracellular network from data remains a very challenging problem in molecular systems biology. Living cells integrate extremely robust circuits that exhibit significant heterogeneity, but still respond to external stimuli in predictable ways. This phenomenon allows us to introduce a network inference methodology that integrates measurements of protein activation from perturbation experiments. The methodology relies on logic-based networks to provide a predictive approximation of the transfer of signals in a network. The approach presented was validated in silico with a set of test networks and applied to investigate the epidermal growth factor receptor signaling of a breast epithelial cell line, MFC10A. In our analysis, we predict the potential signaling circuitry most likely responsible for the experimental readouts of several proteins in the mitogen-activated protein kinase and phosphatidylinositol-3 kinase pathways. The approach can also be used to identify additional necessary perturbation experiments to distinguish between a set of possible candidate networks.

The matricellular protein periostin contributes to proper collagen function and is downregulated during skin aging

BACKGROUND

Periostin is a secreted 90kDa matricellular protein, which is predominantly expressed in collagen-rich tissues. Collagen is the most abundant protein in mammals and has great tensile strength. Recent investigations have shown that periostin influences collagen fibrillogenesis and biomechanical properties of murine connective tissues.

OBJECTIVE

We investigated the function of periostin concerning collagen homeostasis during intrinsic and extrinsic skin aging. For this purpose, human skin samples of young and old donors as well as samples of photoaged and sun-protected skin areas were analyzed for periostin expression. Using in vitro models, we determined the cell types responsible for periostin expression and performed functional analyses with periostin knockdown cells.

METHODS

TaqMan Real-Time PCR, UV irradiation, knockdown experiments, immunostaining, electron microscopy, collagen degradation assay, collagen crosslink analysis.

RESULTS

Periostin expression is highest in the papillary dermis and downregulated during skin aging. Fibroblasts and non-follicular skin derived precursors were identified as main source for periostin expression in human skin. Periostin knockdown in fibroblasts has no effect on collagen expression, but results in an increased fibril diameter and aberrant collagen structure. This leads to an increased susceptibility of collagen toward proteases, whereas recombinant periostin protects collagen fibrils from degradation.

CONCLUSION

Our data show that periostin plays an important role for proper collagen assembly and homeostasis. During skin aging periostin expression decreases and contributes to the phenotype of aged skin.

Abstract 5239: Unraveling the complex regulatory relationship between PI3K signaling and metabolic transformation in breast cancer

Cancer cells exhibit a metabolic phenotype characterized by high rates of glucose uptake and lactate production, known as the Warburg effect. While the Warburg effect and normal proliferative metabolism appear similar, important molecular differences exist. We hypothesize that molecular and metabolic drivers of the Warburg effect can be modulated to impede cancer proliferation without substantial effects on normal tissue growth. Intracellular networks exhibit a variety of emergent non-linear behaviors and, as a result, the use of experimental intuition alone will not be enough to identify these drivers. Using a combination of experimental and theoretical methods, we developed a model of breast cancer progression that includes metabolism and the phosphatidylinositol-3 kinase (PI3K) signaling pathway, an important regulator of carbon metabolism. A key component of our model is a detailed logic network of molecular interactions associated with PI3K signaling as well as regulatory connections to central carbon metabolism, including the ATP/AMP ratio, GLUT receptor activation, hexokinase activation, and changes in the catalytic activity of pyruvate kinase. To validate our model, a series of phospho Western blot analyses were performed using a normal-like breast cell line and a diverse set of breast cancer cell lines exposed to PI3K pathway inhibitors. From these data, a series of predictive network models were constructed representing distinct stages of breast cancer progression. We also generated detailed metabolic flux maps for each cell line using metabolic flux analysis (MFA), a method that relies on carbon-13 tracers, mass-spectrometry, and measurements of extracellular flux to infer intracellular flux. In agreement with recent studies, we found an increase in the reductive carboxylation of glutamine derived alpha-ketoglutarate in cells constitutively adapted to hypoxia. We also identified a potentially important metabolic vulnerability in aggressive breast cancers. Moreover, we found important PI3K network differences at the RNA and protein levels, some of which were isoform specific. Together our data indicate that very different system-level properties are associated with distinct stages of breast cancer progression and metabolic transformation. Our model is suitable for performing in silico molecular perturbations to predict a normal as well as tumor level response to a targeted therapy or combination of therapies. Our approach also serves as a prototype for the use of systems biology methods in personalized medicine where molecular and metabolic data collected from a patient's biopsied tumor is input into a predictive model designed to develop a strategic treatment plan for the patient. The use of predictive models to integrate data from an individual patient will have a profound impact on cancer care decisions and patient outcomes in the future.

Citation Format: Michelle L. Wynn, Megan Egbert, Lauren D. Van Wassenhove, Zhi Fen Wu, Firas Midani, Charles Evans, Charles F. Burant, Santiago Schnell, Sofia D. Merajver. Unraveling the complex regulatory relationship between PI3K signaling and metabolic transformation in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5239. doi:10.1158/1538-7445.AM2013-5239

The effects of tooth extraction on alveolar bone biomechanics in the miniature pig, Sus scrofa

OBJECTIVE

This study investigated the role of occlusion in the development of biomechanical properties of alveolar bone in the miniature pig, Sus scrofa. The hypothesis tested was that the tissues supporting an occluding tooth would show greater stiffness and less strain than that of a non-occluding tooth.

DESIGN

Maxillary teeth opposing the erupting lower first molar (M(1)) were extracted on one side. Occlusion developed on the contralateral side. Serially administered fluorochrome labels tracked bone mineralisation apposition rate (MAR). A terminal experiment measured in vivo buccal alveolar bone strain on occluding and non-occluding sides during mastication. Ex vivo alveolar strains during occlusal loading were subsequently measured using a materials testing machine (MTS/Sintech). Whole specimen stiffness and principal strains were calculated.

RESULTS

MAR tended to be higher on the extraction side during occlusion. In vivo buccal shear strains were higher in the alveolar bone of the occluding side vs. the extraction side (mean of 471 microvarepsilon vs. 281 microvarepsilon, respectively; p=0.04); however, ex vivo shear strains showed no significant differences between sides. Stiffness differed between extraction and occlusion side specimens, significantly so in the low load range (344 vs. 668 MPa, respectively; p=0.04).

CONCLUSIONS

Greater in vivo shear strains may indicate more forceful chews on the occluding side, whereas the similarity in ex vivo bone strain magnitude suggests a similarity in alveolar bone structure and occlusal load transmission regardless of occlusal status. The big overall change in specimen stiffness that was observed was likely attributable to differences in the periodontal ligament rather than alveolar bone.

Outcome analysis of minimally invasive repair of pectus excavatum: review of 251 cases

BACKGROUND/PURPOSE

Since the first report in 1997 by Dr Nuss of the technique for minimally invasive repair of pectus excavatum (MIRPE), the popularity and demand for this operation has increased dramatically. Many pediatric surgeons became familiarized with MIRPE and have applied it to a large number of patients. Outcomes and complications have not yet been defined.

METHODS

A comprehensive survey of APSA members was conducted to review technical problems, complications, and outcomes of this new technique.

RESULTS

Of the 74 survey responders, 31 (42%) currently use the MIRPE as their procedure of choice, and 251 cases were reviewed. A total of 74.2% of surgeons relied on direct observation and written documentation to obtain training in MIRPE. Less than 60% used the chest index in the preoperative assessment. A total of 98% used the Walter Lorenz bar for the MIRPE. The most common complication was bar displacement or rotation requiring reoperation (9.2%). Pneumothorax requiring tube thoracostomy was reported in 4.8%. Less common problems included infectious complications (2%), pleural effusion (2%), thoracic outlet obstruction (0.8%), cardiac injury (0.4%), sternal erosion (0.4%), pericarditis (0.4%), and anterior thoracic artery pseudoaneurysm (0.4%). Three patients (1.2%) required early strut removal. Reoperation using the open modified Ravitch approach was performed in 2 patients (0.8%). Most surgeons indicated that teenaged patients (>15 years old) were at higher risk for complications. Thoracoscopy in combination with MIRPE was used by 61% of the surgeons. Overall patient satisfaction was rated as excellent or good (96.5%).

CONCLUSIONS

The relatively high incidence of problems with MIRPE is probably related to the learning curve associated with the introduction of this new technique. Awareness of technical details, careful patient selection, use of a stabilizing bar, and thoracoscopy likely will result in decreased complications. Long-term results are yet to be determined. The development of a national registry is of great importance for further outcome analysis of MIRPE.

One-stop surgery: evolving approach to pediatric outpatient surgery

PURPOSE

Maximizing patient satisfaction is of prime importance in today's competitive outpatient surgery market. The authors recently devised a system, one-stop surgery, which simplifies outpatient surgery for pediatric patients and their families by combining the traditionally separate preoperative evaluation and subsequent operation into one visit. This report describes our initial experience with one-stop surgery.

METHODS

Umbilical hernia repair, circumcision, and portacath removal were considered surgical procedures appropriate for our one-stop surgery pilot study. Medical information obtained by phone or fax from referring physicians was used to identify potential candidates. Families were contacted, precertified for their surgical procedure, and given nothing by mouth instructions. The day of surgery the child was evaluated by the attending pediatric surgeon. If the diagnosis was confirmed, and no contraindications to surgery were identified, the child immediately underwent the prescheduled surgical procedure.

RESULTS

From April through October 1997, 61 children were scheduled for one-stop surgery. Nine patients (15%) were no shows, and one additional family opted not to proceed with circumcision. The remaining 51 children (83%) underwent their one-stop surgical procedure: umbilical hernia repair (n = 23), circumcision (n = 19), portacath removal (n = 8), and inguinal hernia repair (n = 1). No child had an anesthetic contraindication to surgery, and only one minor postoperative complication (wound hematoma) occurred.

CONCLUSIONS

This pilot study has demonstrated that with appropriate patient screening and cooperation of the entire surgical team, a variety of outpatient surgical procedures can be handled using this one-stop surgery method. By combining one-stop surgery with our previously reported phone follow-up system, many minor surgical procedures can be managed with only one visit to the hospital. Decreasing the "hassle factor" of outpatient surgery for children and their families, who frequently live far from their closest children's hospital, while providing the highest quality of specialized surgical and anesthetic care, may potentially be a very powerful marketing tool for pediatric surgical specialists.

Stability of Le Fort I osteotomy with maxillary advancement: a comparison of combined wire fixation and rigid fixation

PURPOSE

This study compares two types of fixation: intraosseous wires, skeletal suspension wiring, and maxillomandibular fixation (combined wire fixation; CWF) with rigid internal fixation (RIF) in patients who underwent Le Fort I osteotomy to correct maxillary hypoplasia.

MATERIALS AND METHODS

All patients were operated on by the same surgeon using a standard technique, which included bone grafting. The 12 patients in group A were treated with CWF for 4 weeks. Group B was made up of 13 patients who had RIF and training elastics for 4 weeks. Cephalometric analysis using a commercial software package was performed on radiographs that were taken immediately preoperatively (T1), 1 day postoperatively (T2), and at least 1 year postoperatively (T4). The position of the maxilla in relation to the cranial base and Frankfort plane at each time interval was compared.

RESULTS

Postsurgical horizontal change (maxillary position change from T2 to T4) for both groups was in the posterior direction. In group A, six patients had less than 1 mm change, three had 1 to 2 mm change, and three had > 2 mm change. In group B, 10 patients had less than 1 mm change, three had 1 to 2 mm change and 0 had > 2 mm change. Comparison of mean values of groups A and B suggested improved stability with rigid versus wire fixation in the horizontal plane; however, statistical analysis of adjusted mean values showed no significant difference. Vertical changes in maxillary position were also measured from postoperatively to 1 year (T2 to T4). The vertical changes were minimal in those cases of maxillary advancement where no vertical changes were planned; however, there was a statistically significant (P = .0024) improved stability with RIF versus combined wire fixation cases. Comparison of adjusted means showed double the amount of vertical setting 1 year postoperatively in the CWF group.

CONCLUSION

Overall, 22 of 25 patients with horizontal maxillary advancement had excellent stability at 1 year. Observed trends suggest that RIF may have improved stability over CWF.

The "three-piece" osteotomy and interpositional bone graft for augmentation of the atrophic mandible

A study of 20 patients who underwent augmentation of an atrophic mandible by a "three-piece" osteotomy and interpositional bone graft technique is presented. The results show a reduced rate of bone resorption in the posterior regions and a reduced incidence of sensory nerve disturbances in comparison with previous visor/sandwich techniques.

Severe hemorrhage from an arteriovenous malformation of the mandible: report of case

A case of a potentially lethal arteriovenous malformation of the mandibular bone in a 6.5-year-old girl is reported. Diagnosis is often difficult and the AVM may be discovered only when a tooth is extracted. The intent of the preceding report is to alert dental practitioners to the need for immediate control of abnormal bleeding from an extraction socket, because of the potentially lethal consequences. Failure to respond quickly to profuse bleeding of this type could result in the death of the patient by exsanguination.

Comparative dynamics of salmonella infection after primary and secondary challenge of mice exposed to 10 and 23 C

Mortality of mice increased significantly as a result of cold exposure when the animals were challenged orally with Salmonella typhimurium, strain RIA. As reported earlier, cold exposure alone did not kill control animals nor did oral challenge at room temperature. No differences were apparent in the number of Salmonella per gram of liver-spleen, colon, or lung between groups of infected mice housed at 23 and 10 C. The number of bacteria increased equally in liver-spleen samples during the period of increasing mortality in the group housed at 10 C and the period of overt illness in those housed at 23 C. The ability to clear the bloodstream of a secondary intravenous challenge did not seem to be impaired by cold exposure. The bacterial load in the spleen and the rate of change in weight of that organ was equal in animals given a secondary challenge at 10 or 23 C. However, the absolute spleen weight was less in the cold-exposed group as was survival when the secondary challenge was administered 3 days after the primary oral challenge. The studies indicate that endotoxin from S. typhimurium may sensitize mice to the lethal effects of cold exposure. The increase in mortality observed in cold-exposed, infected mice is not due to greater bacterial proliferation in these animals. Rather, the combined stress effects of the bacterial agent(s) and cold may link lympholytic effects to impaired detoxification and increased energy demands, which often leads to lethal vascular collapse in cold-exposed, infected mice.