Assessment of Manufacturing Related Deficiencies for Modified Release Tablet in Abbreviated New Drug Applications.

Generic drugs play an important role in public health. However, the first review cycle approval rate for Abbreviated New Drug Applications (ANDAs) is generally low. To identify if the drug product (DP) manufacturing related deficiencies are the potential root causes of low first review cycle approval of the modified release (MR) tablet ANDAs, we collected and analyzed the review recommendations from each review discipline and the DP manufacturing (process and facility) related deficiencies for original MR tablet ANDAs submitted between FY17 and FY19. We identified 193 original MR tablet ANDAs. The analysis showed that 12% of the applications were approved in first review cycle, while 88% received complete responses (CR). Of the 169 CR applications, 91% were found inadequate for multiple review disciplines. A total of 1345 DP manufacturing process-related deficiencies were issued to 184 ANDAs during the first review cycle. We have identified common deficiencies across ANDAs based on DP manufacturing process categories. The top deficiencies cited reasons include facilities are out of compliance/not ready to commercialize/not ready for inspection; critical process parameter (CPP) ranges are not proposed/proposed CPP ranges are too wide and/or not supported by studied range and no in-process controls (IPCs) are proposed/proposed IPCs acceptance criteria (limits) are too wide and/or not supported by observed data etc. Avoiding the common DP manufacturing deficiencies may reduce the need for issuing DP manufacturing related deficiencies in information requests (IRs), discipline review letters (DRLs), and CRs for MR tablet ANDAs.

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural similarity at the predicted active site with the known members of the GH16 family, with the closest match to the endoglucanase subfamily. The method discussed herein can predict whether an SG protein is correctly or incorrectly annotated and can sometimes provide a reliable functional annotation. Examples of application of the method across folds, comparing active sites between two proteins of different structural folds, are also given.

CDD: NCBI's conserved domain database.

NCBI's CDD, the Conserved Domain Database, enters its 15(th) year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs).

BACKGROUND: The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and to predict function from structure would add tremendous value to structural genomics data. We report on a new method, Structurally Aligned Local Sites of Activity (SALSA), for the prediction of biochemical function based on a local structural match at the predicted catalytic or binding site. RESULTS: Implementation of the SALSA method is described. For the structural genomics protein PY01515 (PDB ID 2aqw) from Plasmodium yoelii, it is shown that the putative annotation, Orotidine 5'-monophosphate decarboxylase (OMPDC), is most likely correct. SALSA analysis of YP_001304206.1 (PDB ID 3h3l), a putative sugar hydrolase from Parabacteroides distasonis, shows that its active site does not bear close resemblance to any previously characterized member of its superfamily, the Concanavalin A-like lectins/glucanases. It is noted that three residues in the active site of the thermophilic beta-1,4-xylanase from Nonomuraea flexuosa (PDB ID 1m4w), Y78, E87, and E176, overlap with POOL-predicted residues of similar type, Y168, D153, and E232, in YP_001304206.1. The substrate recognition regions of the two proteins are rather different, suggesting that YP_001304206.1 is a new functional type within the superfamily. A structural genomics protein from Mycobacterium avium (PDB ID 3q1t) has been reported to be an enoyl-CoA hydratase (ECH), but SALSA analysis shows a poor match between the predicted residues for the SG protein and those of known ECHs. A better local structural match is obtained with Anabaena beta-diketone hydrolase (ABDH), a known ß-diketone hydrolase from Cyanobacterium anabaena (PDB ID 2j5s). This suggests that the reported ECH function of the SG protein is incorrect and that it is more likely a ß-diketone hydrolase. CONCLUSIONS: A local site match provides a more compelling function prediction than that obtainable from a simple 3D structure match. The present method can confirm putative annotations, identify misannotation, and in some cases suggest a more probable annotation.

Profiling the process development of Wurster coating for modified release capsule products in approved drug product applications.

In this paper, we have studied Wurster Coating operation for the manufacture of modified release (MR) capsule products submitted to FDA as New Drug Applications (NDAs) and Abbreviated New Drug Applications (ANDAs) by using a data-driven approach. We have collected and classified information into Wurster coating associated process variables, quality attributes, and scale up strategies under Quality by Design (QbD) paradigm. We have quantified the importance and risk of the process variables and quality attributes by analyzing reported frequencies and risk factors, respectively. We have also included analysis of quality attributes listed with high risk factors, such as weight gain, particle size, assay, dissolution of coated beads, and water content/ Loss on drying (LOD) and the process variables with higher risk factors, such as product temperature, spray rate, atomization air pressure, Inlet air volume and Inlet air temperature, etc. We believe that the knowledge obtained through profiling Wurster coating operation will help the industry to further improve the quality of drug product applications regarding the development of this unit operation. We hope systematic profiling of pharmaceutical unit operations under QbD paradigm can provide support for FDA's IT  initiatives aiming at improving the efficiency and consistency of FDA's quality assessment.

Desulfurization of cysteine-containing peptides resulting from sample preparation for protein characterization by mass spectrometry.

In this study, we have examined two cysteine modifications resulting from sample preparation for protein characterization by mass spectrometry (MS): (1) a previously observed conversion of cysteine into dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine into alanine. Using model peptides, the conversion of cysteine into dehydroalanine via beta-elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37 degrees C, pH 7.0-9.0) without disulfide reduction and alkylation. Furthermore, the surprising conversion of cysteine into alanine was shown to occur by heating cysteine-containing peptides in the presence of a phosphine (tris(2-carboxyethyl)phosphine hydrochloride (TCEP)). The formation of alanine from cysteine, investigated by performing experiments in H(2)O or D(2)O, suggested a radical-based desulfurization mechanism unrelated to beta-elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis.

TAT peptide and its conjugates: proteolytic stability.

The proteolytic cleavage of TATp, TATp-PEG(1000)-PE conjugate (TATp-conjugate), and TATp as TATp-conjugate in mixed micelles made of TATp-conjugate and PEG(5000)-PE (2.5% mol of TATp-conjugate, TATp-Mic) were studied by HPLC with fluorescent detection using fluorenylmethyl chloroformate (FMOC) labeling and by MALDI-TOF MS analysis. The cleavage kinetics were analyzed in human blood plasma and in trypsin-containing phosphate buffered saline (PBS), pH 7.4, to simulate the proteolytic activity of human plasma. The trypsinolysis of free TATp, TATp-conjugate, and TATp-Mic revealed that the main initial fragmentation is an endocleavage at the carboxyl terminus resulting in an Arg-Arg (RR) dimer. The trypsinolysis followed pseudo-first-order kinetics. The cleavage of the free TATp was relatively fast with a half-life of a few minutes (t(1/2) ∼ 3.5 min). The TATp-conjugate showed more stability with about a 3-fold increase in half-life (t(1/2) ∼ 10 min). TATp in TATp-Mic was highly protected against proteolysis with an over 100-fold increase in half-life (t(1/2) ∼ 430 min). The shielding of TATp by PEG moieties in the proposed TATp-Mic is of great importance for its potential use as a cell-penetrating moiety for multifunctional "smart" drug delivery systems with detachable PEG.

Improving the consistency of domain annotation within the Conserved Domain Database.

When annotating protein sequences with the footprints of evolutionarily conserved domains, conservative score or E-value thresholds need to be applied for RPS-BLAST hits, to avoid many false positives. We notice that manual inspection and classification of hits gathered at a higher threshold can add a significant amount of valuable domain annotation. We report an automated algorithm that 'rescues' valuable borderline-scoring domain hits that are well-supported by domain architecture (DA, the sequential order of conserved domains in a protein query), including tandem repeats of domain hits reported at a more conservative threshold. This algorithm is now available as a selectable option on the public conserved domain search (CD-Search) pages. We also report on the possibility to 'suppress' domain hits close to the threshold based on a lack of well-supported DA and to implement this conservatively as an option in live conserved domain searches and for pre-computed results. Improving domain annotation consistency will in turn reduce the fraction of NR sequences with incomplete DAs.

The human Aurora kinase inhibitor danusertib is a lead compound for anti-trypanosomal drug discovery via target repurposing.

New drugs for neglected tropical diseases such as human African trypanosomiasis (HAT) are needed, yet drug discovery efforts are not often focused on this area due to cost. Target repurposing, achieved by the matching of essential parasite enzymes to those human enzymes that have been successfully inhibited by small molecule drugs, provides an attractive means by which new drug optimization programs can be pragmatically initiated. In this report we describe our results in repurposing an established class of human Aurora kinase inhibitors, typified by danusertib (1), which we have observed to be an inhibitor of trypanosomal Aurora kinase 1 (TbAUK1) and effective in parasite killing in vitro. Informed by homology modeling and docking, a series of analogs of 1 were prepared that explored the scope of the chemotype and provided a nearly 25-fold improvement in cellular selectivity for parasite cells over human cells.

Pharmacological validation of Trypanosoma brucei phosphodiesterases B1 and B2 as druggable targets for African sleeping sickness.

Neglected tropical disease drug discovery requires application of pragmatic and efficient methods for development of new therapeutic agents. In this report, we describe our target repurposing efforts for the essential phosphodiesterase (PDE) enzymes TbrPDEB1 and TbrPDEB2 of Trypanosoma brucei , the causative agent for human African trypanosomiasis (HAT). We describe protein expression and purification, assay development, and benchmark screening of a collection of 20 established human PDE inhibitors. We disclose that the human PDE4 inhibitor piclamilast, and some of its analogues, show modest inhibition of TbrPDEB1 and B2 and quickly kill the bloodstream form of the subspecies T. brucei brucei . We also report the development of a homology model of TbrPDEB1 that is useful for understanding the compound-enzyme interactions and for comparing the parasitic and human enzymes. Our profiling and early medicinal chemistry results strongly suggest that human PDE4 chemotypes represent a better starting point for optimization of TbrPDEB inhibitors than those that target any other human PDEs.

pH-responsive core-shell particles and hollow spheres attained by macromolecular self-assembly.

According to our "block-copolymer-free" strategy for self-assembly of polymers, noncovalently connected micelles (NCCM) with poly(epsilon-caprolactone) (PCL) as the core and poly(acrylic acid) (PAA) as the shell in aqueous solutions were attained due to specific interactions between the component polymers. The micellar structure was then locked in by the reaction of PAA with diamine. Afterward, hollow spheres based on PAA network were obtained by either core degradation with lipase or core dissolution with dimethylformamide of the cross-linked micelles. The cavitation process was monitored by dynamic light scattering, which indicated a mass decrease and size expansion. The hollow structure is confirmed by transmission electron microscopy observations. The resultant hollow spheres are pH- and salt-responsive: there is a substantial volume increase when pH changes from acid to base, and vice versa. The volume change takes place dramatically over the pH-range from 5.8 to 7.5. Furthermore, this volume-pH-dependence is found to be completely reversible provided the effect of ionic strength is excluded. The volume change can be adjusted by changing the shell thickness and the cross-linking degree of the hollow spheres. The salt effect on the hollow sphere size depends on pH: with increasing salt concentration the size shows an increase, a decrease, and a little change in acidic, basic, and neutral media, respectively.