Free Energy Perturbation Approach for Accurate Crystalline Aqueous Solubility Predictions

Early assessment of crystalline thermodynamic solubility continues to be elusive for drug discovery and development despite its critical importance, especially for the ever-increasing fraction of poorly soluble drug candidates. Here we present a detailed evaluation of a physics-based free energy perturbation (FEP+) approach for computing the thermodynamic aqueous solubility. The predictive power of this approach is assessed across diverse chemical spaces, spanning pharmaceutically relevant literature compounds and more complex AbbVie compounds. Our approach achieves predictive (RMSE = 0.86) and differentiating power (R2 = 0.69) and therefore provides notably improved correlations to experimental solubility compared to state-of-the-art machine learning approaches that utilize quantum mechanics-based descriptors. The importance of explicit considerations of crystalline packing in predicting solubility by the FEP+ approach is also highlighted in this study. Finally, we show how computed energetics, including hydration and sublimation free energies, can provide further insights into molecule design to feed the medicinal chemistry DMTA cycle.

Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields

Crystal structure prediction (CSP) his generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.

Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior

Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Ų in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.

Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules

Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include calculating the free energy of static lattice phonons, quasi-harmonic approximations (QHA), and computing the full thermodynamic cycle using replica exchange molecular dynamics (REMD). We found that 13 out of the 29 systems minimized from experimental crystal structures restructured to a lower energy minimum when heated and annealed using REMD, a phenomenon that QHA alone cannot capture. Here, we present a series of methods that are intermediate in accuracy and expense between QHA and computing the full thermodynamic cycle, which can save 42-80% of the computational cost and introduces, on this benchmark, a relatively small (0.16 ± 0.04 kcal/mol) error relative to the full thermodynamic cycle. In particular, a method that Boltzmann weights harmonic free energies from along the trajectory of REMD replica exchange appears to be an appropriate intermediate between QHA and the full thermodynamic cycle using MD when screening crystal polymorph stability.

Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion

We present a novel approach to efficiently implement thermal expansion in the quasi-harmonic approximation (QHA) for both isotropic and more importantly, anisotropic expansion. In this approach, we rapidly determine a crystal's equilibrium volume and shape at a given temperature by integrating along the gradient of expansion from 0 Kelvin up to the desired temperature. We compare our approach to previous isotropic methods that rely on a brute-force grid search to determine the free energy minimum, which is infeasible to carry out for anisotropic expansion, as well as quasi-anisotropic approaches that take into account the contributions to anisotropic expansion from the lattice energy. We compare these methods for experimentally known polymorphs of piracetam and resorcinol and show that both isotropic methods agree to within error up to 300 K. Using the Grüneisen parameter causes up to 0.04 kcal/mol deviation in the Gibbs free energy, but for polymorph free energy differences there is a cancellation in error with all isotropic methods within 0.025 kcal/mol at 300 K. Anisotropic expansion allows the crystals to relax into lattice geometries 0.01-0.23 kcal/mol lower in energy at 300 K relative to isotropic expansion. For polymorph free energy differences all QHA methods produced results within 0.02 kcal/mol of each other for resorcinol and 0.12 kcal/mol for piracetam, the two molecules tested here, demonstrating a cancellation of error for isotropic methods. We also find that with expansion in more than a single volume variable, there is a non-negligible rate of failure of the basic approximations of QHA. Specifically, while expanding into new harmonic modes as the box vectors are increased, the system often falls into alternate, structurally distinct harmonic modes unrelated by continuous deformation from the original harmonic mode.

Protective Polymer Coatings for High-Throughput, High-Purity Cellular Isolation

Cell-based therapies are emerging as the next frontier of medicine, offering a plausible path forward in the treatment of many devastating diseases. Critically, current methods for antigen positive cell sorting lack a high throughput method for delivering ultrahigh purity populations, prohibiting the application of some cell-based therapies to widespread diseases. Here we show the first use of targeted, protective polymer coatings on cells for the high speed enrichment of cells. Individual, antigen-positive cells are coated with a biocompatible hydrogel which protects the cells from a surfactant solution, while uncoated cells are immediately lysed. After lysis, the polymer coating is removed through orthogonal photochemistry, and the isolate has >50% yield of viable cells and these cells proliferate at rates comparable to control cells. Minority cell populations are enriched from erythrocyte-depleted blood to >99% purity, whereas the entire batch process requires 1 h and <$2000 in equipment. Batch scale-up is only contingent on irradiation area for the coating photopolymerization, as surfactant-based lysis can be easily achieved on any scale.

Therapeutic intent of proton pump inhibitor prescription among elderly nonsteroidal anti-inflammatory drug users

BACKGROUND

Prescription of proton pump inhibitors (PPIs) has increased dramatically.

AIM

To assess therapeutic intent of PPI prescription among elderly veterans prescribed nonsteroidal anti-inflammatory drugs.

METHODS

Medical-record abstraction identified therapeutic intent of PPI prescription. An 'appropriate therapeutic intent' was defined as symptomatic gastro-oesophageal reflux disease or endoscopic oesophagitis, Zollinger-Ellison disease, dyspepsia, upper gastrointestinal event, Helicobacter pylori infection or nonsteroidal anti-inflammatory drug gastroprotection. Logistic regression predicted the outcome while adjusting for clinical characteristics.

RESULTS

Of 1491 patients [mean 73 years (s.d. 5.6), 73% white and 99.8% men], among those charts which did document a therapeutic indication, 88.8% were appropriate. Prior gastroscopy was predictive of an appropriate therapeutic intent (OR 2.7; 95% CI: 1.9-3.7). Prescription to patients who used VA pharmacy services only, to in-patients, or by a cardiologist or an otolaryngologist were less likely to be appropriate. Gastroprotection was poorly recognized as an indication for PPI prescription, except by rheumatologists (OR 46.7; 95% CI: 15.9-136.9), or among highly co-morbid patients (OR 1.8; 95% CI: 1.1-2.9). Among in-patients, 45% of PPI prescriptions were initiated for unknown or inappropriate reasons.

CONCLUSIONS

Type of provider predicts appropriate PPI use. In-patient prescription is associated with poor recognition of necessary gastroprotection and unknown therapeutic intent.

Identification of Helicobacter pylori infected patients, using administrative data

BACKGROUND

Helicobacter pylori is a prevalent organism implicated in peptic ulcer disease.

AIM

To validate administrative data for diagnosis of H. pylori-infected patients.

METHODS

Administrative data identified patients with ICD-9 code for H. pylori (041.86) or prescription of eradication therapy; diagnosis was confirmed by chart abstraction. Multivariable regression assessed predictors of infection considering drug therapy, ICD-9 code 041.86, procedure code, in-patient or out-patient diagnostic code, age, gender and race to generate an algorithm for validation.

RESULTS

The test cohort of 531 patients (361 potential cases; 170 random controls) was primarily male (94%), Caucasian (59%) and elderly [67 years (s.d. 10)]. The positive predictive value (PPV) of ICD-9 code 041.86 was 100% and 97.4% if from an in-patient or out-patient encounter, respectively. Eradication drug therapy had a PPV of 73.7% (triple therapy) and 97.7% (quadruple therapy). The strongest predictors were out-patient ICD-9 code 041.86 (OR 8.1; 95% CI: 7.0-9.1); eradication drug therapy (OR 7.4; 95% CI: 6.6-8.3); oesophagogastroduodenoscopy (OR 3.5; 95% CI: 3.3-3.6); and age > or =70 (OR 1.2; 95% CI: 1.1-1.4). An algorithm including these data elements yielded a c-statistic of 0.93 and PPV of 97.9%.

CONCLUSIONS

Administrative data can diagnose H. pylori-infected patients. The diagnostic algorithm includes presence of eradication drug therapy overlapping with an out-patient ICD-9 code 041.86 among elderly adults.

National mortality following upper gastrointestinal or cardiovascular events in older veterans with recent nonsteroidal anti-inflammatory drug use

BACKGROUND

Upper gastrointestinal events (UGIE), myocardial infarction (MI) and cerebrovascular accident (CVA) are known morbidities among recent NSAID users.

AIM

To assess all-cause mortality following UGIE, MI or CVA among recent NSAID users.

METHODS

Veterans >65 prescribed an NSAID at any Veterans Affairs (VA) facility were identified using prescription fill data and their records linked to a merged VA-Medicare database. Each person-day was assessed for NSAID, coxib or proton pump inhibitor (PPI) exposure. Incidence density ratios and hazard rates of death were calculated following UGIE, MI and CVA adjusting for demographics, co-morbidity, prescription channeling, geographic location and pharmacological covariates.

RESULTS

Among 474 495 patients [97.8% male; 85.3% white; 73.9 years (s.d. 5.6)], death followed at a rate of 5.5 per 1000 person-years (95% CI: 5.4-5.6) post-UGIE, 17.7 per 1000 person-years (95% CI: 17.5-17.9) post-MI and 21.8 per 1000 person-years (95% CI: 21.6-22.0) post-CVA. CVA was associated with greatest risk of death [hazard ratio (HR) 12.4; 95% CI: 10.9-14.3] followed by MI (HR 10.7; 95% CI: 9.2-11.6) and UGIE (HR 3.3; 95% CI: 2.8-3.9). Predictors of mortality were advancing age and co-morbidity, increased use of coxibs and failure to ensure adequate gastroprotection.

CONCLUSION

Among elderly veterans with recent NSAID use, an UGIE, MI or CVA is a clinically relevant premorbid event.

Cyclooxygenase-2 selectivity of non-steroidal anti-inflammatory drugs and the risk of myocardial infarction and cerebrovascular accident

AIM

To assess degree of cyclooxygenase-2 (COX-2) selectivity of a non-steroidal anti-inflammatory drug (NSAID) and risk of myocardial infarction (MI) or cerebrovascular accident (CVA).

METHODS

Prescription fill data were linked to medical records of a merged VA-Medicare dataset. NSAIDs were categorized by Cox-2 selectivity. Incidence of CVA and MI within 180 days of index prescription was assessed using Cox-proportional hazards models adjusted for gender, race, cardiovascular and pharmacological risk factors and propensity for prescription of highly COX-2 selective NSAIDs.

RESULTS

Of 384,322 patients (97.5% men and 85.4% white), 79.4% were prescribed a poorly selective, 16.4% a moderately selective and 4.2% a highly selective NSAID. There were 985 incident cases of MI and 586 cases of CVA in >145 870 person-years. Highly selective agents had the highest rate of MI (12.3 per 1000 person-years; [95% CI: 12.2-12.3]) and CVA (8.1 per 1000 person-years; [95% CI: 8.0-8.2]). Periods without NSAID exposure were associated with lowest risk. In adjusted models, highly selective COX-2 selective NSAIDs were associated with a 61% increase in CVA and a 47% increase in MI, when compared with poorly selective NSAIDs.

CONCLUSIONS

The risk of MI and CVA increases with any NSAID. Highly COX-2 selective NSAIDs confer the greatest risk.

Validation of administrative data used for the diagnosis of upper gastrointestinal events following nonsteroidal anti-inflammatory drug prescription

AIMS

To validate veterans affairs (VA) administrative data for the diagnosis of nonsteroidal anti-inflammatory drug (NSAID)-related upper gastrointestinal events (UGIE) and to develop a diagnostic algorithm.

METHODS

A retrospective study of veterans prescribed an NSAID as identified from the national pharmacy database merged with in-patient and out-patient data, followed by primary chart abstraction. Contingency tables were constructed to allow comparison with a random sample of patients prescribed an NSAID, but without UGIE. Multivariable logistic regression analysis was used to derive a predictive algorithm. Once derived, the algorithm was validated in a separate cohort of veterans.

RESULTS

Of 906 patients, 606 had a diagnostic code for UGIE; 300 were a random subsample of 11 744 patients (control). Only 161 had a confirmed UGIE. The positive predictive value (PPV) of diagnostic codes was poor, but improved from 27% to 51% with the addition of endoscopic procedural codes. The strongest predictors of UGIE were an in-patient ICD-9 code for gastric ulcer, duodenal ulcer and haemorrhage combined with upper endoscopy. This algorithm had a PPV of 73% when limited to patients >or=65 years (c-statistic 0.79). Validation of the algorithm revealed a PPV of 80% among patients with an overlapping NSAID prescription.

CONCLUSIONS

NSAID-related UGIE can be assessed using VA administrative data. The optimal algorithm includes an in-patient ICD-9 code for gastric or duodenal ulcer and gastrointestinal bleeding combined with a procedural code for upper endoscopy.

Predicting which patients can resume oral nutrition after percutaneous endoscopic gastrostomy tube placement

BACKGROUND

Percutaneous endoscopic gastrostomy tubes are placed with high frequency and relative safety for a variety of indications. One of these indications is temporary nutritional support for patients expected to resume oral nutrition.

AIMS

To determine if baseline clinical characteristics can predict which patients attain the clinical goal of resuming oral nutrition with consequent tube removal.

METHODS

We conducted a single site observational cohort study from December 1999 to April 2001, enrolling all patients scheduled for percutaneous endoscopic gastrostomy placement. Standard descriptive and bivariate analyses were performed. Cox proportional hazard models were constructed to identify patient characteristics prior to percutaneous endoscopic gastrostomy placement that might predict resumption of oral nutrition with tube removal.

RESULTS

Bivariate analyses revealed four potential clinical predictors: age < 65 years, localized head and neck cancer, serum albumin > or = 3.75 g/dL, and serum creatinine < or = 1.1 mg/dL. In multivariable analysis, age < 65 years (HR = 3.7, 95% CI: 1.0-14.3) and a diagnosis of localized head and neck cancer (HR = 4.6, 95% CI: 1.4-15.0) predicted resumption of oral nutrition with percutaneous endoscopic gastrostomy removal.

CONCLUSIONS

When discussing percutaneous endoscopic gastrostomy placement, doctors should consider the likelihood of achieving clinically important outcomes such as the resumption of oral nutrition with tube removal. This clinical goal is unlikely for older patients with diagnoses other than localized head and neck cancer.

Increased use of low anterior resection for veterans with rectal cancer

BACKGROUND

Two surgical procedures with curative intent are available to patients with rectal cancer: lower anterior resection and abdominoperineal resection; however, lower anterior resection may improve quality of life and functional status.

AIM

To examine temporal changes in after lower anterior resection and abdominoperineal resection between 1989 and 2000. Potential factors associated with the use of lower anterior resection were evaluated.

METHODS

Using national administrative data, we identified patients who received lower anterior resection or abdominoperineal resection. Logistic regression models examined the association between use of lower anterior resection and time period of surgical resection.

RESULTS

A total of 5201 rectal cancer patients underwent resection. The use of lower anterior resection increased from 40.0% (1989-91) to 50.1% (1998-2000) paralleled by a corresponding decline in abdominoperineal resection (60.1 to 49.9%; P < 0.001). Patients who received surgery during 1992-94, 1995-97 and 1998-2000 were 6, 7 and 28% more likely to receive lower anterior resection, when compared with 1989-1991 after adjusting for demographic characteristics, co-morbidity and hospital surgical volume. Older age, lower co-morbidity score and lower hospital surgical volume were predictive of lower anterior resection.

CONCLUSIONS

An increase in the use of lower anterior resection for rectal cancer was observed over time. This observed increase in use is not confined to high-volume hospitals.

Meta-analysis of short-term outcomes after laparoscopic resection for colorectal cancer

BACKGROUND

The safety and efficacy of laparoscopic resection (LR) for colorectal cancer remains to be established.

METHODS

A meta-analysis of randomized clinical trials comparing the short-term outcomes of laparoscopic with those of open resection for colorectal cancer was undertaken. A literature search was performed for relevant articles published by the end of 2002. Two reviewers independently appraised the trials using a predetermined protocol. Results were analysed using Comprehensive Meta-analysis.

RESULTS

The outcomes of 2512 procedures from 12 trials were analysed. LR took on average 32.9 per cent longer to perform than open resection but was associated with lower morbidity rates. Specifically, wound infection rates were significantly lower (odds ratio 0.47 (95 per cent confidence interval 0.28 to 0.80); P = 0.005). In patients undergoing LR, the average time to passage of first flatus was reduced by 33.5 per cent, that to tolerance of a solid diet by 23.9 per cent and that to 80 per cent recovery of peak expiratory flow by 44.3 per cent. Early narcotic analgesia requirements were also reduced by 36.9 per cent, pain at rest by 34.8 per cent and during coughing by 33.9 per cent, and hospital stay by 20.6 per cent. There were no significant differences in perioperative mortality or oncological clearance.

CONCLUSION

LR for colorectal cancer is associated with lower morbidity, less pain, a faster recovery and a shorter hospital stay than open resection, without compromising oncological clearance.

Systematic review: the methodological quality of trials affects estimates of treatment efficacy in functional (non-ulcer) dyspepsia

AIM

To evaluate treatment efficacy using objective quality criteria.

METHODS

A systematic review was performed of randomized controlled trials of endoscopically investigated dyspepsia (1979-2003) using the Jadad score and Rome II guidelines. The Jadad score differentiated studies as 'high quality' (score 4-5/5) vs. 'poor quality' (score 1-3/5). Three key Rome II guidelines on study design (cut-off of 0/3 or > 0/3) were also compared with the Jadad score.

RESULTS

Poor quality trials suggested a benefit of prokinetic therapy [relative risk (RR) of remaining dyspeptic, 0.47; 95% confidence interval (CI), 0.39-0.56), which was not confirmed in high quality trials (RR, 1.0; 95% CI, 0.84-1.19). There was a marked benefit of H2-receptor antagonist therapy in poor quality trials (RR, 0.68; 95% CI, 0.61-0.76), but a marginal benefit in good quality trials (RR, 0.87; 95% CI, 0.79-0.97). Trial quality did not affect the small statistically significant benefit seen with Helicobacter pylori eradication. Two high quality trials suggested a limited benefit with the use of proton pump inhibitors, with no poor quality trials to provide a comparison. Separation of the studies by the Rome II criteria had a similar impact on the calculated treatment estimates.

CONCLUSIONS

The magnitude of benefit of prokinetic and H2-receptor antagonist therapies reported in previous meta-analyses has been over-estimated. The quality of trials has an impact on the efficacy estimates of treatment. The Rome II criteria for study methodology may be appropriate for judging study quality.

Selective cannulation of the common bile duct: a prospective randomized trial comparing standard catheters with sphincterotomes

BACKGROUND

Current recommendations for the use of standard catheters or sphincterotomes for the initial attempt at selective common bile duct cannulation have been made in the absence of prospective comparative data.

METHODS

A prospective study was carried out in which patients were randomized to undergo cannulation with a standard catheter or a sphincterotome (standard or wire-guided). Multivariate models were constructed to determine significant independent predictors of the success rates of initial and selective cannulation and the number of attempts and time needed to achieve selective cannulation.

RESULTS

Eighty-three successive patients were evaluated; 36 were excluded because they had undergone previous therapeutic endoscopic retrograde cholangiopancreatography (ERCP) or a Billroth II operation. Of the 47 patients (28 women, mean age 60.6 +/- 14.5 years), indications for ERCP included suspected bile duct stones in 41 patients, pancreatico-biliary malignancies in 4, and biliary leaks in 2. Eighteen patients were randomized to undergo selective common bile duct cannulation with standard catheter and 29 to standard/wire-guided sphincterotome. Initial common bile duct cannulation for the standard catheter and standard/wire-guided sphincterotome groups was successful in 12 (67% [95% CI: 41%, 87%]) and 28 (97% [95% CI: 82%, 100%]) patients, respectively (95% CI for the difference: -0.57 to -0.03, p = 0.009). Using intention to treat analysis, selective common bile duct cannulation was successful for standard catheter and standard/wire-guided sphincterotome patients in 17 (94% [95% CI: 73%, 99%]) and 28 (97% [95% CI: 82%, 100%]) cases, respectively (95% CI for the difference: -0.15 to +0.10, p > 0.05). The mean number of attempts required to achieve selective common bile duct cannulation were 12.4 +/- 6.0 and 2.8 +/- 3.1 (p = 0.0001). The mean time taken to achieve selective common bile duct cannulation was 13.5 +/- 6.14 and 3.1 +/- 5.1 minutes (p = 0.0001). Multivariate modeling revealed that the initial choice of catheter was the only significant independent predictor of the time taken and the number of attempts performed to achieve selective common bile duct cannulation (p = 0. 0001 for each model).

CONCLUSION

The use of standard/wire-guided sphincterotome was superior to that of standard catheter for the initial attempt at cannulation of the common bile duct. The number of attempts required may bear clinical significance with regard to the development of post-ERCP pancreatitis and warrants further study.