Bayer's in silico ADMET platform: a journey of machine learning over the past two decades.

Over the past two decades, an in silico absorption, distribution, metabolism, and excretion (ADMET) platform has been created at Bayer Pharma with the goal to generate models for a variety of pharmacokinetic and physicochemical endpoints in early drug discovery. These tools are accessible to all scientists within the company and can be a useful in assisting with the selection and design of novel leads, as well as the process of lead optimization. Here.

Discovery of Rogaratinib (BAY 1163877): a pan-FGFR Inhibitor.

Rogaratinib (BAY 1163877) is a highly potent and selective small-molecule pan-fibroblast growth factor receptor (FGFR) inhibitor (FGFR1-4) for oral application currently being investigated in phase 1 clinical trials for the treatment of cancer. In this publication, we report its discovery by de novo structure-based design and medicinal chemistry optimization together with its pharmacokinetic profile.

Novel TIE-2 inhibitor BAY-826 displays in vivo efficacy in experimental syngeneic murine glioma models.

Targeting the vascular endothelial growth factor signaling axis in glioblastoma inevitably leads to tumor recurrence and a more aggressive phenotype. Therefore, other angiogenic pathways, like the angiopoietin/tunica interna endothelial cell kinase (TIE) signaling axis, have become additional targets for therapeutic intervention. Here, we explored whether targeting the receptor tyrosine kinase TIE-2 using a novel, highly potent, orally available small molecule TIE-2 inhibitor (BAY-826) improves tumor control in syngeneic mouse glioma models.

Best of both worlds: combining pharma data and state of the art modeling technology to improve in Silico pKa prediction.

In a unique collaboration between a software company and a pharmaceutical company, we were able to develop a new in silico pKa prediction tool with outstanding prediction quality. An existing pKa prediction method from Simulations Plus based on artificial neural network ensembles (ANNE), microstates analysis, and literature data was retrained with a large homogeneous data set of drug-like molecules from Bayer. The new model was thus built with curated sets of ∼14,000 literature pKa values (∼11,000 compounds, representing literature chemical space) and ∼19,500 pKa values experimentally determined at Bayer Pharma (∼16,000 compounds, representing industry chemical space).

CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory.

CypScore is an in silico approach for predicting the likely sites of cytochrome P450-mediated metabolism of druglike organic molecules. It consists of multiple models for the most important P450 oxidation reactions such as aliphatic hydroxylation, N-dealkylation, O-dealkylation, aromatic hydroxylation, double-bond oxidation, N-oxidation, and S-oxidation. Each of these models is based on atomic reactivity descriptors derived from surface-based properties calculated with ParaSurf and based on AM1 semiempirical molecular orbital theory.

Design and synthesis of potent and selective azaindole-based Rho kinase (ROCK) inhibitors.

Rho kinase plays a pivotal role in several cellular processes such as vasoregulation, making it a suitable target for the treatment of hypertension and related disorders. We discovered a new compound class of Rho kinase (ROCK) inhibitors containing a 7-azaindole hinge-binding scaffold tethered to an aminopyrimidine core. Herein we describe the structure-activity relationships elucidated through biochemical and functional assays.

Cardiovascular effects of a novel potent and highly selective azaindole-based inhibitor of Rho-kinase.

Background And Purpose: Rho-kinase (ROCK) has been implicated in the pathophysiology of altered vasoregulation leading to hypertension. Here we describe the pharmacological characterization of a potent, highly selective and orally active ROCK inhibitor, the derivative of a class of azaindoles, azaindole 1 (6-chloro-N4-{3,5-difluoro-4-[(3-methyl-1H-pyrrolo[2,3-b]pyridin-4-yl)oxy]-phenyl}pyrimidine-2,4-diamine).

Experimental Approach: Pharmacological characterization of azaindole 1 was performed with human recombinant ROCK in vitro.

In silico ADMET traffic lights as a tool for the prioritization of HTS hits.

The need for in silico characterization of HTS hit structures as part of a data-driven hit-selection process is demonstrated. A solution is described in the form of an in silico ADMET traffic light and PhysChem scoring system. This has been extensively validated with in-house data at Bayer, published data, and a collection of launched small-molecule oral drugs.

Creating the environment for a successful community partnership.

This paper describes the development of the American Indian Oncology Program (AIOP) and presents the accomplishments of a participatory research approach that involved an integrated network for cancer care and research. AIOP used a participatory process to develop infrastructure, identify research questions, develop methodologies, write supplemental grants, and evaluate accomplishments based on community defined measures of success. Partnerships between University and Indian Health Service, private, and state institutions led to improved collaboration.

Transcriptosome and serum cytokine profiling of an atypical case of myelodysplastic syndrome with progression to acute myelogenous leukemia.

A Native American-Indian female presenting with anemia and thrombocytosis was diagnosed with myelodysplastic syndrome (MDS, refractory anemia). Over the course of 5 years she developed cytopenias and periods of leukocytosis with normal bone marrow (BM) blast counts, features of an unclassifiable MDS/MPS syndrome. The patient ultimately progressed to acute myelogenous leukemia (AML, FAB M2) and had a normal karyotype throughout her course.

Improving the hit-to-lead process: data-driven assessment of drug-like and lead-like screening hits.

Drug-like and lead-like hits derived from HTS campaigns provide good starting points for lead optimization. However, too strong emphasis on potency as hit-selection parameter might hamper the success of such projects. A detailed absorption, distribution, metabolism, excretion and toxicology (ADME-Tox) profiling is needed to help identify hits with a minimum number of (known) liabilities.

In silico prediction of aqueous solubility, human plasma protein binding and volume of distribution of compounds from calculated pKa and AlogP98 values.

We have investigated whether three important ADME (absorption, distribution, metabolism, excretion) related properties (aqueous solubility, human plasma protein binding, and human volume of distribution at steady-state) can be predicted from chemical structure alone if only the predicted predominant ionisation state and lipophilicity (calculated logP [P = octanol-water partition coefficient]) are considered. A simple, fast method for the in silico prediction of aqueous solubility of predominantly uncharged compounds has been developed, while some potential is shown for the prediction of predominantly charged or zwitterionic compounds. Ten other known in silico prediction methods for aqueous solubility have also been evaluated.

Molecular characterization of the principal substrate binding site of the ubiquitous folding catalyst protein disulfide isomerase.

Disulfide bond formation in the endoplasmic reticulum of eukaryotes is catalyzed by the ubiquitously expressed enzyme protein disulfide isomerase (PDI). The effectiveness of PDI as a catalyst of native disulfide bond formation in folding polypeptides depends on the ability to catalyze disulfide-dithiol exchange, to bind non-native proteins, and to trigger conformational changes in the bound substrate, allowing access to buried cysteine residues. It is known that the b' domain of PDI provides the principal peptide binding site of PDI and that this domain is critical for catalysis of isomerization but not oxidation reactions in protein substrates.

A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases.

The pK(a) values of the CXXC active-site cysteine residues play a critical role in determining the physiological function of the thioredoxin superfamily. To act as an efficient thiol-disulphide oxidant the thiolate state of the N-terminal cysteine must be stabilised and the thiolate state of the C-terminal cysteine residue destabilised. While increasing the pK(a) value of the C-terminal cysteine residue promotes oxidation of substrates, it has an inhibitory effect on the reoxidation of the enzyme, which is promoted by the formation of a thiolate at this position.

Correlates of mammogram density in southwestern Native-American women.

Little is known about the breast cancer risk factors or mammogram characteristics among Native-American women. Southwestern Native-American women have a low risk of breast cancer and a high risk of diabetes. Our purpose was to determine the prevalence of known clinical risk factors for breast cancer and their association with mammogram density in a sample of Southwestern Native-American women undergoing breast cancer screening.

Recent advances in the prediction of blood-brain partitioning from molecular structure.

The widely distributed software tools Cerius2 and ACD/log D Suite have been used to develop a new method for the prediction of the ratio of concentrations of a drug in the brain and blood (BB,quantified as log BB) from structure. The performances of all known blood-brain partitioning prediction methods are compared to give an up-to-date account on their accuracy, limitations, and usefulness. It is demonstrated that the new log BB prediction method is superior to other methods with regard to low-to-medium throughput log BB prediction, whereas the C2-ADME log BB two-dimensional (2D) method seems to offer the best compromise between speed and accuracy for ultra-high throughput processing of large compound databases for log BB prediction.

Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor.

Peptide deformylase (PDF) is an essential bacterial metalloenzyme which deformylates the N-formylmethionine of newly synthesized polypeptides and as such represents a novel target for antibacterial chemotherapy. To identify novel PDF inhibitors, we screened a metalloenzyme inhibitor library and identified an N-formyl-hydroxylamine derivative, BB-3497, and a related natural hydroxamic acid antibiotic, actinonin, as potent and selective inhibitors of PDF. To elucidate the interactions that contribute to the binding affinity of these inhibitors, we determined the crystal structures of BB-3497 and actinonin bound to Escherichia coli PDF at resolutions of 2.

Barriers to cancer screening in Mexican-American women.

Objective: To test the simultaneous effect of various established predictors of breast and cervical cancer screening (breast self-examination, clinical breast examination by a physician, Papanicolaou [Pap] smear, and pelvic examination) in a low-income, Mexican-American sample.

Material And Methods: A total of 188 Mexican-American women participated in a face-to-face structured interview in their preferred language. We tested a model with four established predictors of breast and cervical cancer screening--communication skills, knowledge of cancer, access to health care (finances and availability of care), and anxiety about cancer.

The breast: in-plane x-ray protection during diagnostic thoracic CT--shielding with bismuth radioprotective garments.

Purpose: To evaluate the ability of thin overlying bismuth radioprotective shielding to reduce the x-ray dose to radiosensitive superficial organs during diagnostic computed tomography (CT).

Materials And Methods: A variety of patient and phantom studies were performed with four thicknesses of bismuth radioprotective latex over the breast. Dose savings were determined with thermoluminescent dosimeters.

Homoharringtonine-induced hyperglycemia.

Homoharringtonine (HHT) has been reported to induce hyperglycemia. This report describes a study conducted to characterize the effect of HHT on insulin production and action. Our data indicate that HHT-induced hyperglycemia results from the development of insulin resistance.

Lymphocyte aggregation in response to adrenergic stimulation.

A nonanemic chronic lymphocytic leukemia patient with nearly 500,000 lymphocytes/microL underwent leukapheresis when she presented with CNS symptoms and retinal vascular engorgement. Respiratory distress developed during the cell separator run, which led us to ask whether the procedure could have changed the adhesive properties of her cells. C5a desarginine, N-f-Met-Leu-Phe, adenosine diphosphate, and collagen all failed to aggregate her lymphocytes in vitro, but arachidonic acid, excess free calcium, and 4 mumol/L epinephrine did aggregate the cells.

Refined chromosome study helps define prognostic subgroups in most patients with primary myelodysplastic syndrome and acute myelogenous leukaemia.

Based on a 6 1/2-year study of 284 consecutive adult patients with primary myelodysplastic syndrome (MDS) and and acute myelogenous leukaemia (AML), we have found that refined chromosome analysis can be used as an independent prognostic indicator in the great majority of patients with MDS and AML. In MDS, the FAB subtype was also found to have prognostic value and this was enhanced when the chromosomal findings were taken into consideration. In AML, the age of the patient correlated more closely with the chromosomal changes in predicting prognosis in most patients than did the FAB classification.

Excretion of hydroxyurea into milk.

This article documents that hydroxyurea (HUR) is excreted into human breast milk, and it reviews the literature describing similar evaluations for other antineoplastic agents.

Cytarabine-induced cerebellar syndrome: case report and literature review.

High-dose cytarabine (HDARAC) therapy is an effective regimen in treating refractory leukemias. A typical regimen is cytarabine 3 g/m2 iv over one to three hours q 12h for a total of 8 to 12 doses. This case report illustrates the neurotoxicity unique to HDARAC.

Refined chromosome analysis as an independent prognostic indicator in de novo myelodysplastic syndromes.

In a study of 56 consecutive adult patients with de novo myelodysplastic syndromes (MDS), all cases were successfully analyzed with two refined chromosome banding techniques. Most patients (44 of 56, 79%) were found to have a chromosome defect. The majority of these patients had a recurrent loss of chromosomal material rather than a reciprocal translocation or inversion, as commonly found in acute leukemia.