Application of Artificial Intelligence and Machine Learning in Drug Discovery.

Machine Learning (ML) and Deep Learning (DL) are two subclasses of Artificial Intelligence (AI), that, in this day and age of big data provides significant opportunities to pharmaceutical discovery research and development by translating data to information and ultimately to knowledge. Machine Learning or AI is not really new but over last few years, application of better methods have emerged and they have been successfully applied for drug discovery and development. This chapter would provide an overview of these methods and how they have been applied across various work streams, e.g., generative chemistry, ADMET prediction, retrosynthetic analysis, etc. within drug discovery process. This chapter would also attempt to provide caution and pit falls in utilizing these methods blindly while summarizing challenges and limitations.

An Overview of Machine Learning and Big Data for Drug Toxicity Evaluation.

Drug toxicity evaluation is an essential process of drug development as it is reportedly responsible for the attrition of approximately 30% of drug candidates. The rapid increase in the number and types of large toxicology data sets together with the advances in computational methods may be used to improve many steps in drug safety evaluation. The development of in silico models to screen and understand mechanisms of drug toxicity may be particularly beneficial in the early stages of drug development where early toxicity assessment can most reduce expenses and labor time. To facilitate this, machine learning methods have been employed to evaluate drug toxicity but are often limited by small and less diverse data sets. Recent advances in machine learning methods together with the rapid increase in big toxicity data such as molecular descriptors, toxicogenomics, and high-throughput bioactivity data may help alleviate some of the current challenges. In this article, the most common machine learning methods used in toxicity assessment are reviewed together with examples of toxicity studies that have used machine learning methodology. Furthermore, a comprehensive overview of the different types of toxicity tools and data sets available to build in silico toxicity prediction models has been provided to give an overview of the current big toxicity data landscape and highlight opportunities and challenges related to them.

Effects of intravitreal bevacizumab in Gram-positive and Gram-negative models of ocular inflammation.

BACKGROUND: Exogenous endophthalmitis is a potential complication of intraocular surgery and frequently results in visual impairment. Current treatment involves administration of intravitreal (IVT) antibiotics with or without vitrectomy surgery. Evidence for the use of adjunctive anti-inflammatory agents is conflicting. We set out to determine if bevacizumab, a humanized monoclonal IgG1 antibody targeted against vascular endothelial growth factor (VEGF), has anti-inflammatory properties in experimental models of Gram-positive and Gram-negative inflammation. METHODS: BALB/c mice were subjected to lipopolysaccharide- (LPS) or peptidoglycan- (PGN) induced ocular inflammation and treated with IVT bevacizumab. Iris microvasculature was imaged 6 hours following irritant/treatment using intravital microscopy (IVM) before the mice were euthanized and the eyes were enucleated immediately post-mortem. Following enucleation, levels of VEGF and 23 cytokines and chemokines (IL-1α, IL-1ß, IL-2, IL-3, IL-4, IL-5, IL-6, IL-10, IL-12 (p40), IL-12 (p70), IL-13, IL-17, TNF, KC, G-CSF, GM-CSF, Eotaxin, INF-γ, MCP-1, MIP-1α, MIP-1ß, RANTES) were quantified using a multiplex assay. RESULTS: Levels of VEGF were significantly increased during the inflammatory response, triggered by either PGN or LPS. Both the adherence of leukocytes to the iris vascular endothelium and the levels of pro-inflammatory cytokines and chemokines were significantly increased following administration of either irritant. Treatment with bevacizumab decreased levels of leukocyte adherence in LPS-treated eyes, however, not in PGN-treated eyes. Conversely, bevacizumab treatment decreased levels of cytokines and chemokines (TNF, IL-6, MCP-1, MIP-1α, MIP-1ß, RANTES, KC) in PGN-treated eyes, however, not in LPS-treated eyes. CONCLUSIONS: Within a 6-hour window bevacizumab had anti-inflammatory actions that were distinct in both Gram-positive (PIU) and Gram-negative (EIU) models, respectively. Given our findings, this would suggest that bevacizumab may have utility as an adjunctive therapy to IVT antibiotics and vitrectomy in the management of exogenous endophthalmitis.

Prevalence and risk factors for kidney stones in fibrodysplasia ossificans progressiva.

The worldwide prevalence and risk factors for kidney stones in patients with fibrodysplasia ossificans progressiva (FOP) are unknown. We conducted a survey of 383 patient-members of the International Fibrodysplasia Ossificans Progressiva Association, comprising the entire global membership of the international FOP community. Two hundred seven patients from 31 nations and 6 continents (54%) responded. Nineteen of 207 respondents had kidney stones, revealing a worldwide prevalence of 9.2%. In a confirmatory follow-up study of subjects participating in a longitudinal FOP natural history study, 9 of 114 individuals reported a history of kidney stones (7.9%). In both study populations patients with kidney stones were found to be more functionally impaired compared to those without nephrolithiasis. The prevalence of kidney stones in the adult FOP population of the Unites States was 15.8% (9/57 individuals) compared to a sex- and age-weighted prevalence of 4.5% (p=4×10-5) in the general population. Although geographical variation exists, patients with FOP have an approximately three-fold greater prevalence of kidney stones than the general population. This unusually high prevalence may be due to high bone turnover from chronic immobilization, or to unknown mechanistic effects of the activating FOP mutation in activin A receptor, type I/activin-like kinase-2 (ACVR1/ALK2), increasing the disease burden and morbidity in this already disabling condition.

Axial strain enhances osteotomy repair with a concomitant increase in connexin43 expression.

The mechanical environment is known to influence fracture healing. We speculated that connexin43 (Cx43) gap junctions, which impact skeletal homeostasis, fracture healing and the osteogenic response to mechanical load, may play a role in mediating the response of the healing bone to mechanical strain. Here, we used an established rat fracture model, which uses a 2 mm osteotomy gap stabilized by an external fixator, to examine the impact of various cyclical axial loading protocols (2%, 10%, and 30% strain) on osteotomy healing. We examined the presence of Cx43 in the osteotomy-healing environment and assessed how mechanical strain modulates Cx43 expression patterns in the callus. We demonstrated that increased cyclical axial strain results in increased radiographic and histologic bone formation. In addition, we show by immunohistochemistry that Cx43 is abundantly expressed in the healing callus, with the expression most robust in samples exposed to increased cyclical axial strain. These data are consistent with the concept that an increase in Cx43 expression by mechanical load may be part of the mechanisms by which mechanical forces enhances fracture healing.

The effects of primary implant bearing design on the complexity of revision unicondylar knee arthroplasty.

Comparisons of fixed- (FB) and mobile-bearing (MB) implants have failed to demonstrate a superiority of one design over the other. Despite showing equally successful outcomes, the wear patterns and small particulate debris associated with MB implants have been linked to an increased prevalence of osteolysis. This study compared the complexity of revision surgery for both bearing types. Operative time, use of augmentation and/or bone grafts, and the level of constraint required during revision were used to assess complexity. It was found that MB knees more frequently required tibial augmentation in our sample population (P=0.020), but overall surgical complexity was equivalent for revisions of both implant designs. These data suggest that additional research pertaining to the potential differences between implants be investigated.

Role of primary bearing type in revision total knee arthroplasty.

Although it has been shown that mobile- and fixed-bearing (FB) prostheses yield equivalent functional outcomes, wear patterns and debris types associated with mobile-bearing (MB) knees have been correlated to an increased prevalence of osteolysis. The complexity of revision surgery was compared between both designs. Several markers, including operative time, use of augmentation, bone grafts, and level of constraint, were analyzed. Data support that for failed total knee arthroplasty, there is a significant difference in mean time to revision between the MB (54.7 months) and FB types (80.6 months) (p ≤ 0.0001). MB knees more frequently required hinged implants during revision, potentially increasing the complexity of the procedure. This study raises concern for use of the MB implants, especially in younger patients who are more likely to require a future revision.

ALOHA: a novel probability fusion approach for scoring multi-parameter drug-likeness during the lead optimization stage of drug discovery.

Automated lead optimization helper application (ALOHA) is a novel fitness scoring approach for small molecule lead optimization. ALOHA employs a series of generalized Bayesian models trained from public and proprietary pharmacokinetic, absorption, distribution, metabolism, and excretion, and toxicology data to determine regions of chemical space that are likely to have excellent drug-like properties. The input to ALOHA is a list of molecules, and the output is a set of individual probabilities as well as an overall probability that each of the molecules will pass a panel of user selected assays. In addition to providing a summary of how and when to apply ALOHA, this paper will discuss the validation of ALOHA's Bayesian models and probability fusion approach. Most notably, ALOHA is demonstrated to discriminate between members of the same chemical series with strong statistical significance, suggesting that ALOHA can be used effectively to select compound candidates for synthesis and progression at the lead optimization stage of drug discovery.

The transcriptional activity of osterix requires the recruitment of Sp1 to the osteocalcin proximal promoter.

The transcription factor osterix (Osx/Sp7) is required for osteogenic differentiation and bone formation in vivo. While Osx can act at canonical Sp1 DNA-binding sites and/or interact with NFATc1 to cooperatively regulate transcription in some osteoblast promoters, little is known about the molecular details by which Osx regulates osteocalcin (OCN) transcription. We previously identified in the OCN proximal promoter a minimal C/T-rich motif, termed OCN-CxRE (connexin-response element) that binds Sp1 and Sp3 in a gap junction-dependent manner. In the present study, we hypothesized that Osx could act via this non-canonical Sp1/Sp3-binding element to regulate OCN transcription. OCN promoter luciferase reporter assays show that Osx alone is an insufficient activator that requires Sp1, but not Sp3, to synergistically stimulate OCN promoter activity. Moreover, promoter deletion analyses demonstrate that both the Sp1/Sp3-binding OCN-CxRE (-70 to -57) and the -92 to -87 region of the OCN proximal promoter are critical for Osx/Sp1 synergistic activities. Our data show that Sp1 influences Osx activity by enhancing Osx occupancy on the OCN promoter, perhaps via physical interactions between the two transcription factors. Finally, alteration of the expression of the gap junction protein connexin43 modulates the recruitment of both Sp1 and Osx to the OCN promoter. In total, our data are strongly in support of Sp1 as an essential transcription factor required for Osx recruitment and transactivation of the OCN promoter. Further, these data lend insight into a mechanism by which alteration of connexin43 impacts osteogenesis in vitro and in vivo.

Induction of an osteocyte-like phenotype by fibroblast growth factor-2.

The purpose of this study was to characterize the molecular phenotype that occurs during the profound morphological shift of cultured osteogenic cells upon treatment with fibroblast growth factor-2 (FGF2). A time course of treatment with FGF2 was performed on an osteoblast cell line, primary bone marrow stromal cells and an osteocyte-like cell line. Morphologic changes were recorded, and gene profiling was carried out by real time PCR. By 8h of FGF2 treatment, there is a striking morphological shift of osteoblast and stromal cells to an elongated dendritic-like morphology that is remindful of osteocytes. In osteoblasts treated with FGF2, this morphologic shift is preceded by an induction of several osteocyte markers, including dentin matrix protein 1 (>20-fold) and E11 (>5-fold). There is a transient increase in the gene expression of sclerostin (3.5-fold) and PHEX (2.5-fold). Sclerostin regulation by FGF2 is complex, as gene expression becomes markedly inhibited by FGF2 at times points after 8h of treatment before rebounding at day 12. Analogous modulation of osteocyte markers is seen in bone marrow stromal cells and MLO-Y4 osteocyte-like cells. In conclusion, this study shows that FGF2 can regulate the transition of osteogenic cells towards the osteocyte lineage, as well as, regulate the expression of critical genes in osteocytes.

An "Omics" based survey of human colon cancer.

Despite an increased understanding of the molecular pathogenesis of colorectal cancer (CRC) during the past two decades, reliable and robust biomarkers to enable screening, surveillance, and primary prevention of this disease are lacking. CRC diagnosis and therapy remain dependent upon descriptive classification and staging systems, based primarily on morphology and histology. The traditional approach of understanding complex biological systems by studying smaller, discrete units of the whole system has been less fruitful for understanding complex diseases. The implicit assumption of traditional methods, that a single or even only a few factors, play a dominant role in a complex disease might be inadequate when studying multifactorial diseases such as cancer. The burgeoning field of systems biology adopts a holistic approach, wherein the integration of individual parts of the system is sought. The cornerstone of a systems biology approach has been the development of a variety of high-throughput "omics" sciences, including genomics, transcriptomics, proteomics, and metabolomics. This review will focus on the "omics" literature in the field of sporadic human CRC and present examples of how a systems approach has been extremely useful in understanding concepts that would have been difficult to develop using traditional methods.

Chemical space: missing pieces in cheminformatics.

Cheminformatics is at a turning point, the pharmaceutical industry benefits from using the various methods developed over the last twenty years, but in our opinion we need to see greater development of novel approaches that non-experts can use. This will be achieved by more collaborations between software companies, academics and the evolving pharmaceutical industry. We suggest that cheminformatics should also be looking to other industries that use high performance computing technologies for inspiration. We describe the needs and opportunities which may benefit from the development of open cheminformatics technologies, mobile computing, the movement of software to the cloud and precompetitive initiatives.

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

Distal humeral fracture with associated triceps tendon avulsion in a renal transplant recipient.

Although distal humeral fractures are well described in the literature, concomitant distal triceps avulsion has not previously been reported. One population that warrants a high index of suspicion for tendon injury after trauma is patients with renal disease. Clinical tests on such patients may yield equivocal results, and in that setting, magnetic resonance imaging may be useful in the diagnosis of concomitant tendon injury. Postoperative rehabilitation is a challenge considering that the old standard of care for isolated triceps avulsions is several weeks of immobilization and that early motion is recommended for open reduction and internal fixation of distal humeral fractures. More recent literature supports early active-assisted range-of-motion (ROM) elbow exercises after triceps tendon repair, and our case supports those recommendations.A 48-year-old, right-hand-dominant man, who was a living-related kidney transplant recipient 3 years previously, presented with radiographic evidence of an intra-articular distal humeral fracture. The patient was rejecting his kidney at the time of injury and was receiving 50 mg of prednisone daily. The patient underwent open reduction and internal fixation of the distal humeral fracture and concomitant triceps repair. Postoperatively, active-assisted and passive ROM elbow exercises were begun. At 3-year follow-up, the patient had 10 degrees to 120 degrees of motion at the elbow, with full supination and pronation.

Scientific evidence for the use of modern patellofemoral arthroplasty.

Patellofemoral arthroplasty has been utilized as a treatment for isolated patellofemoral arthritis for more than 30 years. However, the use of this procedure remains controversial, as many surgeons prefer to use total knee arthroplasty, even for isolated patellofemoral arthritis. While historically, the results with this procedure have been inconsistent, recent developments in prosthesis design and surgical indications have improved the outcomes of patellofemoral arthroplasty. Potential advantages of patellofemoral arthroplasty include a less invasive approach, less bone resection, less tissue destruction, shorter operative time, less blood loss, shorter rehabilitation, and more normal knee kinematics. However, proper indications and surgical technique are crucial in order to obtain optimal results. Some future modifications have the potential to further improve the outcomes of the procedure, although additional investigations are needed to further explore some of these aspects. This report will describe current knowledge regarding the indications and contraindications for patellofemoral arthroplasty, present the results and complications of this procedure, discuss alternative treatments for patellofemoral disease, and explore future directions for arthroplasty of the patellofemoral compartment.

Use of small intestine submucosa in a rat model of acute and chronic rotator cuff tear.

Augmentation materials for rotator cuff tears, such as small intestine submucosa (SIS), have been used with the goal of improving outcome. Knowledge is limited on the use of SIS in animal models of acute and chronic rotator cuff tears. We hypothesized that the use of SIS in the surgical management of full thickness supraspinatus tears would improve histologic and biomechanical properties. Results show temporal improvements in several histologic parameters. Both acute and chronic injuries repaired with SIS have similar and increased mechanical properties respectively, compared to those repaired without SIS. In general, acute repairs with SIS were comparable to acute repairs without SIS. In chronic repairs, the use of SIS significantly reduced the cross sectional area of the healing tendon and increased the modulus. These results provide information on the use of SIS for rotator cuff repairs.

The contribution of methotrexate exposure and host factors on transcriptional variance in human liver.

Long-term administration of methotrexate (MTX) for management of chronic inflammatory diseases is associated with risk of liver damage. In this study, we examined the transcriptional profiles of livers from patients treated with MTX. The possibility that expression signatures correlate with grade of fibrosis or underlying rheumatic disease was evaluated. Twenty-seven patients taking MTX were accrued for this study. Ten non-MTX-exposed normal liver specimens were used as controls. Global mRNA expression was assayed using oligonucleotide arrays. A total of 205 genes were significantly altered in MTX-exposed livers. Six of these genes were validated by qPCR. Two genes, CLN8 and ANKH that map to chromosomal locations previously associated with rheumatoid arthritis, were found to be elevated in MTX-exposed samples. Subsequent pathway analysis indicates that MTX exposure is associated with the following key alterations: (1) upregulation of lipid biosynthetic genes, consistent with MTX-induced steatosis, (2) downregulation of proinflammatory chemokines, consistent with the anti-inflammatory effects of MTX, and (3) elevation of complement pathway gene expression. Complement 5, shown earlier to be correlated with liver fibrosis in mice, was found to be elevated (twofold) in MTX-exposed livers. In conclusion, we have found the expression of a number of genes associated with rheumatic disease and/or MTX exposure to be significantly different. Differences in complement expression provide the rationale for future correlative studies between MTX-induced liver fibrosis and C5 alleles in order to identify patients with increased risk for fibrosis.

Expression profile of osteoblast lineage at defined stages of differentiation.

The inherent heterogeneity of bone cells complicates the interpretation of microarray studies designed to identify genes highly associated with osteoblast differentiation. To overcome this problem, we have utilized Col1a1 promoter-green fluorescent protein transgenic mouse lines to isolate bone cells at distinct stages of osteoprogenitor maturation. Comparison of gene expression patterns from unsorted or isolated sorted bone cell populations at days 7 and 17 of calvarial cultures revealed an increased specificity regarding which genes are selectively expressed in a subset of bone cell types during differentiation. Furthermore, distinctly different patterns of gene expression associated with major signaling pathways (Igf1, Bmp, and Wnt) were observed at different levels of maturation. Some of our data differ from current models of osteoprogenitor cell differentiation and emphasize components of the pathways that were not revealed in studies based on a total cell population. Thus, applying methods to generate more homogeneous populations of cells at a defined level of cellular differentiation from a primary osteogenic culture is feasible and leads to a novel interpretation of the gene expression associated with increasing levels of osteoprogenitor maturation.