TALAPRO-3 clinical trial protocol: phase III study of talazoparib plus enzalutamide in metastatic castration-sensitive prostate cancer

Poly(ADP-ribose) polymerase inhibitors in combination with androgen-receptor signaling inhibitors are a promising therapeutic option for patients with metastatic castration-sensitive prostate cancer (mCSPC) and homologous recombination repair (HRR) gene alterations. Here, we describe the design and rationale of the multinational, phase III, TALAPRO-3 study comparing talazoparib plus enzalutamide versus placebo plus enzalutamide in patients with mCSPC and HRR gene alterations. The primary end point is investigator-assessed radiographic progression-free survival (rPFS) per RECIST 1.1 in soft tissue, or per PCWG3 criteria in bone. The TALAPRO-3 study will demonstrate whether the addition of talazoparib can improve the efficacy of enzalutamide as assessed by rPFS in patients with mCSPC and HRR gene alterations undergoing androgen deprivation therapy. Clinical Trial Registration:NCT04821622 (ClinicalTrials.gov) Registry Name: Study of Talazoparib With Enzalutamide in Men With DDR Gene Mutated mCSPC. Date of Registration: 29 March 2021.

Neoadjuvant Talazoparib in Patients With Germline BRCA1/2 Mutation-Positive, Early-Stage Triple-Negative Breast Cancer: Results of a Phase II Study

BACKGROUND

The undetermined efficacy of the current standard-of-care neoadjuvant treatment, anthracycline/platinum-based chemotherapy, in patients with early-stage triple-negative breast cancer (TNBC) and germline BRCA mutations emphasizes the need for biomarker-targeted treatment, such as poly(ADP-ribose) polymerase inhibitors, in this setting. This phase II, single-arm, open-label study evaluated the efficacy and safety of neoadjuvant talazoparib in patients with germline BRCA1/2-mutated early-stage TNBC.

PATIENTS AND METHODS

Patients with germline BRCA1/2-mutated early-stage TNBC received talazoparib 1 mg once daily for 24 weeks (0.75 mg for moderate renal impairment) followed by surgery. The primary endpoint was pathologic complete response (pCR) by independent central review (ICR). Secondary endpoints included residual cancer burden (RCB) by ICR. Safety and tolerability of talazoparib and patient-reported outcomes were assessed.

RESULTS

Of 61 patients, 48 received ≥80% talazoparib doses, underwent surgery, and were assessed for pCR or progressed before pCR assessment and considered nonresponders. pCR rate was 45.8% (95% confidence interval [CI], 32.0%-60.6%) and 49.2% (95% CI, 36.7%-61.6%) in the evaluable and intent-to-treat (ITT) population, respectively. RCB 0/I rate was 45.8% (95% CI, 29.4%-63.2%) and 50.8% (95% CI, 35.5%-66.0%) in the evaluable and ITT population, respectively. Treatment-related adverse events (TRAE) were reported in 58 (95.1%) patients. Most common grade 3 and 4 TRAEs were anemia (39.3%) and neutropenia (9.8%). There was no clinically meaningful detriment in quality of life. No deaths occurred during the reporting period; 2 deaths due to progressive disease occurred during long-term follow-up (>400 days after first dose).

CONCLUSIONS

Neoadjuvant talazoparib monotherapy was active despite pCR rates not meeting the prespecified threshold; these rates were comparable to those observed with combination anthracycline- and taxane-based chemotherapy regimens. Talazoparib was generally well tolerated.

CLINICALTRIALS.GOV IDENTIFIER

NCT03499353.

Hot crystals of thermo-responsive particles with temperature dependent diameter in the presence of a temperature gradient

Structure formation under non-equilibrium steady state conditions is poorly understood. A non-equilibrium steady state can be achieved in a system by maintaining a temperature gradient. A class of cross-linked microgel particles, such as poly-N-iso-propylacrylamide, is reported to increase in size due to the adsorption of water as the temperature decreases. Here, we study thermo-responsive particles with a temperature sensitive diameter in the presence of a temperature gradient, using molecular dynamics simulations with the Langevin thermostat. We find long-ranged structural order using bond order parameters in both cold and hot regions of the system beyond a certain diameter ratio of the cold and hot particles. This is due to an increase in packing and pressure in both regions. Our observations might be useful in understanding ordered structures under extreme conditions of a non-equilibrium steady state.

Paediatric Strategy Forum for medicinal product development of DNA damage response pathway inhibitors in children and adolescents with cancer: ACCELERATE in collaboration with the European Medicines Agency with participation of the Food and Drug Administration

DNA damage response inhibitors have a potentially important therapeutic role in paediatric cancers; however, their optimal use, including patient selection and combination strategy, remains unknown. Moreover, there is an imbalance between the number of drugs with diverse mechanisms of action and the limited number of paediatric patients available to be enrolled in early-phase trials, so prioritisation and a strategy are essential. While PARP inhibitors targeting homologous recombination-deficient tumours have been used primarily in the treatment of adult cancers with BRCA1/2 mutations, BRCA1/2 mutations occur infrequently in childhood tumours, and therefore, a specific response hypothesis is required. Combinations with targeted radiotherapy, ATR inhibitors, or antibody drug conjugates with DNA topoisomerase I inhibitor-related warheads warrant evaluation. Additional monotherapy trials of PARP inhibitors with the same mechanism of action are not recommended. PARP1-specific inhibitors and PARP inhibitors with very good central nervous system penetration also deserve evaluation. ATR, ATM, DNA-PK, CHK1, WEE1, DNA polymerase theta and PKMYT1 inhibitors are early in paediatric development. There should be an overall coordinated strategy for their development. Therefore, an academia/industry consensus of the relevant biomarkers will be established and a focused meeting on ATR inhibitors (as proof of principle) held. CHK1 inhibitors have demonstrated activity in desmoplastic small round cell tumours and have a potential role in the treatment of other paediatric malignancies, such as neuroblastoma and Ewing sarcoma. Access to CHK1 inhibitors for paediatric clinical trials is a high priority. The three key elements in evaluating these inhibitors in children are (1) innovative trial design (design driven by a clear hypothesis with the intent to further investigate responders and non-responders with detailed retrospective molecular analyses to generate a revised or new hypothesis); (2) biomarker selection and (3) rational combination therapy, which is limited by overlapping toxicity. To maximally benefit children with cancer, investigators should work collaboratively to learn the lessons from the past and apply them to future studies. Plans should be based on the relevant biology, with a focus on simultaneous and parallel research in preclinical and clinical settings, and an overall integrated and collaborative strategy.

TALAPRO-3: A phase 3, double-blind, randomized study of enzalutamide (ENZA) plus talazoparib (TALA) vs placebo plus ENZA in patients with DDR gene-mutated, metastatic castration-sensitive prostate cancer (mCSPC)

TPS279

Background: TALA is a poly(ADP-ribose) polymerase inhibitor (PARPi) that has shown efficacy in metastatic castration-resistant prostate cancers with alterations in DNA damage response (DDR) genes involved directly or indirectly in homologous recombination repair (HRR). ENZA is an androgen receptor (AR) inhibitor and established therapy for mCSPC. Since PARP activity has been shown to support AR function, PARP inhibition may increase sensitivity to AR-directed therapies. In addition, AR blockade downregulates HRR gene regulation, which has been hypothesized to induce a “ BRCAness” phenotype. These studies suggest that TALA in combination with ENZA may significantly improve clinical outcomes for men with mCSPC and DDR-HRR alterations. The phase 3, double-blind, randomized trial TALAPRO-3 (NCT04821622) herein presented will compare the combination of TALA plus ENZA vs placebo plus ENZA in this setting. Methods: Approximately 550 patients with mCSPC harboring DDR-HRR alterations will be randomized to TALA (0.5 mg once daily [QD]) plus ENZA (160 mg QD) or placebo (once daily) plus ENZA (160 mg QD). Patients will be stratified according to de novo mCSPC vs relapsed mCSPC, high-volume disease vs low-volume disease, where high-volume disease is defined as the presence of visceral metastases or ≥4 bone lesions with ≥1 beyond the vertebral bodies and pelvis, and BRCA vs non-BRCA mutational status. Key eligibility criteria include age ≥18 years; histological diagnosis of prostate cancer; alterations in at least one of 12 DDR/HRR genes known to sensitize patients to PARPi ( ATM, ATR, BRCA1, BRCA2, CDK12, CHEK2, FANCA, MLH1, MRE11A, NBN, PALB2, RAD51C); and metastatic disease (no brain metastases). Primary endpoint is radiographic progression-free survival (defined as time to radiographic progression in soft tissue per Response Evaluation Criteria in Solid Tumors version 1.1 or in bone per Prostate Cancer Working Group 3 criteria by investigator, or death). Secondary endpoints include overall survival, safety, and patient-reported outcomes. Patient recruitment is planned/ongoing at approximately 285 sites in 27 countries, including the US and Europe, South America, South Africa, and Asia-Pacific. As of 30 September 2022, a total of 319 patients have been randomized in the study. This study was approved by an Institutional Review Board. Clinical trial information: NCT04821622 .

Conformational fluctuations in the molten globule state of α-lactalbumin

A molten globule (MG) state is an intermediate state of a protein observed during the unfolding of the native structure. The MG state of the protein is induced by various denaturing agents (like urea), extreme pH, pressure, and heat. Experiments suggest that the MG state of some proteins is functionally relevant even if there is no well-defined tertiary structure. Earlier experimental and theoretical studies show that the MG state of a protein is dynamic in nature, where conformational states are interconverted on nanosecond time scales. These observations lead us to study and compare the conformational fluctuations of the MG state to those of intrinsic disordered proteins (IDPs). We consider a milk protein, α-lactalbumin (aLA), which shows an MG state at low pH upon removal of the calcium (Ca²⁺) ion. We use the constant pH molecular dynamics (CpHMD) simulation to maintain the protonation state of titratable residues at a low pH during the simulation. We use the dihedral principal component analysis, the density based clustering method, and the machine learning technique to identify the conformational fluctuations. We observe metastable states in the MG state. The residues containing the essential coordinates responsible for metastability belong to a stable helix in the crystal structure, but most of them prefer unstructured or bent conformation in the MG state. These residues control the exposure of the putative binding residues for fatty acids. Thus, the MG state of a protein behaves as an intrinsic disorder protein, although the disorder here is induced by external conditions.

TALAPRO-3: A phase 3, double-blind, randomized study of enzalutamide (ENZA) plus talazoparib (TALA) versus placebo plus ENZA in patients with DDR gene–mutated, metastatic castration-sensitive prostate cancer (mCSPC)

TPS5096

Background: TALA is a poly(ADP-ribose) polymerase inhibitor (PARPi) approved as monotherapy for germline BRCA1/2-mutated HER2-negative advanced breast cancer. Clinical efficacy in metastatic castration-resistant prostate cancers (mCRPC) with alterations in DNA damage response (DDR) genes involved directly or indirectly in homologous recombination repair (HRR) has been demonstrated with some PARPi. Phase 3 study findings (de Bono et al. N Engl J Med, 2020;382:2091-2102) resulted in the approval of olaparib for mCRPC. ENZA is an androgen receptor (AR) inhibitor and established therapy for mCSPC. Since PARP activity has been shown to support AR function, PARP inhibition may increase sensitivity to AR-directed therapies. In addition, AR blockade downregulates HRR gene regulation, which has been hypothesized to induce a “ BRCAness” phenotype. A Phase 2 study of TALA monotherapy (TALAPRO-1) demonstrated robust antitumor activity in men with heavily pretreated, HRR-mutated mCRPC. The Phase 3, double-blind, randomized trial TALAPRO-3 (NCT04821622) herein presented will compare the combination of TALA plus ENZA vs placebo plus ENZA in men with mCSPC with DDR/HRR alterations. Methods: Approximately 550 patients with mCSPC harboring DDR/HRR alterations will be randomized to TALA (0.5 mg once daily) plus ENZA (160 mg once daily) or placebo (once daily) plus ENZA (160 mg once daily). Patients will be stratified according to de novo mCSPC vs relapsed mCSPC, high-volume disease vs low-volume disease, where high-volume disease is defined as the presence of visceral metastases or ≥4 bone lesions with ≥1 beyond the vertebral bodies and pelvis and BRCA vs non-BRCA mutational status. Key eligibility criteria include age ≥18 years; histological diagnosis of prostate cancer; alterations in at least one of 12 DDR/HRR genes known to sensitize patients to PARPi ( ATM, ATR, BRCA1, BRCA2, CDK12, CHEK2, FANCA, MLH1, MRE11A, NBN, PALB2, RAD51C); and metastatic disease (no brain metastases). Primary endpoint is rPFS (time to radiographic progression in soft tissue per RECIST 1.1 or in bone per PCWG3 criteria by investigator, or death). Secondary endpoints include overall survival, safety, and patient-reported outcomes. Patient recruitment is planned at approximately 285 sites in 27 countries, including the US and Europe, South America, South Africa, and Asia-Pacific. This study was approved by an Institutional Review Board. Clinical trial information: NCT04821622.

Viscoelastic response of fluid trapped between two dissimilar van der Waals surfaces

Employing grand canonical Monte-Carlo and molecular dynamics simulations, the viscoelastic response of trapped fluid under molecularly thin confinement by walls having different wall-fluid interaction strengths, is investigated. With increase in slit asymmetry, given by the ratio of interaction strengths of the wall having strong wall-fluid interaction to that of the wall with weak wall-fluid interaction, a crossover in effective density of the fluid film, from rarer (R) to denser (D) than the bulk density is observed. Upon increasing asymmetry further, the dense fluid (F) layers undergo bond-orientational (S) ordering. The variation of viscoelastic relaxation time with scaled asymmetry shows a universal behavior, independent of slit width, with two distinct regimes. Below a critical value of asymmetry, the viscoelastic relaxation time is a slowly varying function of asymmetry, comparable with the structural relaxation time. Beyond the critical asymmetry, on the other hand, viscoelastic response time shows a sharp increase upon increasing asymmetry, deviating markedly from the structural relaxation time. Interestingly the critical asymmetry value is found to correlate with R to D crossover. The microscopic origin of the two-regime universal behavior of viscoelastic response time is found to stem from the fact that below critical asymmetry, the overall viscoelastic behaviour of the slit is dominated by that of the fast relaxing layer close to the weakly attracting surface, while above the critical asymmetry, the relaxation behaviour is guided by the dense fluid layer adjacent to the strongly attracting wall. In vicinity of fluid to ordering transition, the loss and storage moduli merge for low frequencies as in gel-like mechanical behaviour. The storage modulus takes over the loss modulus in the phase co-existence region even before the long ranged order sets in. Our findings bear important implications for fluid transport in hetero-structured geometry in nanotechnology.

Evaluation of pharmacokinetics and safety of talazoparib in patients with advanced cancer and varying degrees of hepatic impairment

AIM

This phase I study investigated talazoparib pharmacokinetics (PK) and safety in patients with advanced solid tumors and varying degrees of hepatic function.

METHODS

Patients with advanced solid tumors and normal hepatic function or varying degrees of hepatic impairment (mild, moderate, and severe, based on NCI-ODWG classification) received talazoparib 0.5 mg once daily for 22 calendar days. Plasma and urine samples after single and multiple doses were collected and analyzed for talazoparib using validated assays. Plasma PK data from all patients were analyzed using population PK method. Plasma and urine PK parameters in PK-evaluable patients were calculated using non-compartmental analysis (NCA). Safety was monitored in all enrolled patients.

RESULTS

38 patients were enrolled; 37 had ≥1 PK concentration, among which 17 were evaluable for NCA. Population PK analysis (n = 37) indicated no significant impact of hepatic function on apparent clearance (CL/F) of talazoparib. Baseline creatinine clearance was the only significant covariate on CL/F (α=0.05). NCA of data (n = 17) showed no clear trend for increase in exposure on Day 22 with worsening hepatic function. Talazoparib protein binding was comparable in patients with varying hepatic function. Talazoparib was generally well tolerated, and the safety profile observed in this study was consistent with the known safety profile of the drug.

CONCLUSIONS

Hepatic impairment (mild, moderate, and severe) has no impact on PK of talazoparib. No dose modification is recommended for patients with advanced solid tumors and various degrees of hepatic impairment, and this labeling language has been approved by US FDA and the EMA.

Talapro-3: A phase 3, double-blind, randomized study of enzalutamide (ENZA) plus talazoparib (TALA) versus placebo plus enza in patients with DDR gene mutated metastatic castration-sensitive prostate cancer (mCSPC)

TPS221

Background: TALA is a poly(ADP-ribose) polymerase inhibitor (PARPi) approved as monotherapy for germline BRCA1/2-mutated HER 2-negative advanced breast cancer. PARPi have demonstrated substantial clinical efficacy in metastatic castration-resistant prostate cancers (mCRPC) with alterations in DNA damage response (DDR) genes involved directly or indirectly in homologous recombination repair (HRR). Phase 3 study findings (de Bono et al. N Engl J Med. 2020;382:2091-2102) resulted in the approval of olaparib for mCRPC. ENZA is an androgen receptor (AR) inhibitor and established therapy for mCSPC. Since PARP activity has been shown to support AR function, PARP inhibition is expected to increase sensitivity to AR-directed therapies. In addition, AR blockade downregulates HRR gene regulation, which has been hypothesized to induce a “ BRCAness ” phenotype . A phase 2 study of TALA monotherapy (TALAPRO-1) demonstrated robust antitumor activity in men with heavily pretreated, HRR-mutated mCRPC . The Phase 3, double-blind, randomized trial TALAPRO-3 (NCT04821622) herein presented will compare the combination of TALA plus ENZA versus placebo plus ENZA in men with mCSPC with DDR/HRR alterations. Methods: Approximately 550 patients with mCSPC harboring DDR/HRR alterations will be randomized to TALA (0.5 mg once daily) plus ENZA (160 mg once daily) or placebo (once daily) plus ENZA (160 mg once daily). Key eligibility criteria include age ≥18 years; histological diagnosis of prostate cancer; alterations in 12 DDR/HRR genes known to sensitize to PARPi ( ATM, ATR, BRCA1, BRCA2, CDK12, CHEK2, FANCA, MLH1, MRE11A, NBN, PALB2, RAD51C); and metastatic disease (no brain metastases). Primary endpoint is rPFS (time to radiographic progression in soft tissue per RECIST 1.1 or in bone per PCWG3 criteria by investigator, or death). Secondary endpoints include overall survival, safety, and patient-reported outcomes. Patient recruitment is planned at approximately 285 sites in 27 countries, including the US and Europe, South America, South Africa, and Asia-Pacific. Clinical trial information: NCT04821622.

A long-range order in a thermally driven system with temperature-dependent interactions

Aggregation of macro-molecules under an external force is far from being understood. An important driving situation is achieved by temperature difference. Inter-particle interactions in metallic nanoparticles with ligand capping are reported to be sensitive to temperature and the zeta potential of the particles being reduced in the cold region. Such particles form aggregates in the cold region of the system in the presence of temperature difference. Here we study the aggregation of particles in the presence of temperature difference with temperature-dependent interaction parameters using Brownian dynamics simulation. The particle interaction and particle diffusion are considered to be sensitive to the local temperature. We identify a long-range structural order in the cold region of the system using the Avrami equation for crystal growth kinetics. Our observations might be useful in designing ordered structures with macro-molecules under non-equilibrium steady-state conditions.

Neoadjuvant talazoparib in patients with germline BRCA1/2 (gBRCA1/2) mutation-positive, early HER2-negative breast cancer (BC): Results of a phase 2 study

505

Background: Talazoparib (TALA) is a poly(ADP-ribose) polymerase inhibitor approved as monotherapy for treating adult patients (pts) with g BRCA1/2-mutated HER2-negative locally advanced or metastatic BC. Methods: This phase 2, non-randomized, single-arm, open-label study (NCT03499353) evaluated the efficacy and safety of TALA in the neoadjuvant setting for pts with early g BRCA1/2-mutated HER2− BC. Primary endpoint was evaluation of pathologic complete response (pCR) as assessed by Independent Central Review (ICR) after completing 24 weeks of neoadjuvant TALA monotherapy 1 mg QD (0.75 mg for moderate renal impairment) followed by surgery. Secondary endpoints included pCR by investigator (INV) and residual cancer burden (RCB) by ICR (RCB: 0 [pCR], I [minimal], II [moderate], III [extensive]). The evaluable population included pts who received at least 80% of the TALA dose prescribed at treatment start and underwent breast surgery and pCR assessment, plus those who progressed before pCR could be assessed. The intent-to-treat (ITT) population included all pts who received at least 1 dose of TALA. Results: Of 61 pts treated with TALA (ITT and safety populations), 48 comprised the evaluable population. All pts had triple-negative BC. 60 pts had adenocarcinoma and 1 had squamous cell histology, with the following staging: I=20, II=27, III=14. Mean age was 44.6 years, mean duration of 4.5 wks since disease onset, mean duration of treatment of 23.3 wks, and mean overall relative dose intensity of 84.5% (ITT population). pCR (assessed by ICR and INV) and RCB (by ICR) for the evaluable and ITT populations are shown in the table below. Ten (16.4%) patients discontinued treatment due to progressive disease. One pt had a disruption of treatment as a result of COVID-19 restrictions, 2 pts for other reasons: to undergo surgery early and consent withdrawal; 9 patients received <80% dose. Treatment-emergent adverse events (AEs) were reported in 98.4% of pts (27.9% grade [G] 1, 23.0% G2, 45.9% G3, 1.6% G4); the most common were fatigue (78.7%; G1 54.1%; G2 21.3%; G3 3.3%), nausea (68.9%; G1 54.1%; G2 13.1%; G3 1.6%), and alopecia (57.4%; G1 54.1%; G2 3.3%). Three (4.9%) pts discontinued treatment due to AEs (G3 anemia [n=2] and G3 vertigo [n=1]) and continued on study. Conclusions: TALA monotherapy in the neoadjuvant setting was active and showed pCR rates comparable to those observed with combination anthracycline and taxane-based chemotherapy regimens and was generally well tolerated. Clinical trial information: NCT03499353. [Table: see text]

The Effect of Renal Impairment on the Pharmacokinetics and Safety of Talazoparib in Patients with Advanced Solid Tumors

Background

Pharmacokinetic (PK) studies suggest that talazoparib is primarily eliminated unchanged via renal excretion. The current study investigated how varying degrees of renal impairment may affect the PK of talazoparib, and evaluated the safety and tolerability of talazoparib, in patients with advanced solid tumors with/without renal impairment.

Methods

Patients with advanced solid tumors and normal renal function or different degrees of renal impairment measured by estimated glomerular filtration rate (eGFR: mild = 60–89, moderate = 30–59, severe = 15–29 mL/min/1.73 m²) were enrolled in this open-label, non-randomized, phase I study. Talazoparib was administered orally at 0.5 mg/day for 22 days. Primary PK parameters included the area under the plasma concentration-time curve from 0 to 24 h (AUC_0–24) and maximum observed plasma concentration (C_max) at steady state (Day 22). Safety and tolerability were also investigated.

Results

Thirty-four patients were enrolled. At Day 22, compared with patients with normal renal function (n = 9), patients with mild (n = 9), moderate (n = 8), or severe (n = 8) renal impairment had a 12.2%, 43.0%, and 163.3% increase in talazoparib AUC_0–24, and a 11.1%, 31.6%, and 89.3% increase in talazoparib C_max, respectively. Talazoparib was generally well tolerated, and overall there were no notable differences in the treatment-emergent adverse event profile across renal function groups.

Conclusions

Exposure to talazoparib increased with worsening renal impairment. Overall, this study confirms current dosing recommendations in patients with mild and moderate renal impairment (1 mg/day and 0.75 mg/day, respectively) and indicates that a lower starting dose of 0.5 mg/day should be considered for patients with severe renal impairment.

Clinical Trials Registration

NCT02997163.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40262-020-00983-y.

Length-scales of dynamic heterogeneity in a driven binary colloid

Here we study the characteristic length scales in an aqueous suspension of a symmetric oppositely charged colloid subjected to a uniform electric field by Brownian dynamics simulations. We consider the in-plane structure in the presence of a sufficiently strong electric field where the like charges in the system form macroscopic lanes. We construct spatial correlation functions characterizing the structural order and that of particles of different mobilities in the plane transverse to the electric field at a given time. We call these functions equal time density correlation functions (ETDCFs). The ETDCFs between particles of different charges, irrespective of mobilities, are the structural ETDCFs, while those between particles of different mobilities are the dynamic ETDCFs. We extract the characteristic length of correlation by fitting the envelopes of the ETDCFs to exponential dependences. We find that the correlation length scales of the structural ETDCFs and the dynamic ETDCFs of the slow particles increase with time in a concurrent manner. This suggests that the clustering of particles tends to build up dynamically correlated slow particles in the plane transverse to the lanes. The ETDCFs can be measured for colloidal systems by directly following the particle motion by video-microscopy and may be useful to understand the patterns out of equilibrium.

Dynamics of water trapped in transition metal oxide-graphene nano-confinement

Motivated by practical implementation of transition-metal oxide-graphene heterostructures, we use all atom molecular dynamics simulations to study dynamics of water in a nano slit bounded by a transition metal oxide surface, namely, TiO2termination of SrTiO3, and graphene. The resultant asymmetric, strong confinement produces square ice-like crystallites of water pinned at TiO2surface and drives enhanced hydrophobicity of graphene via the proximity effect to the hydrophilic TiO2surface. This importantly brings in dynamic heterogeneity, both in translational and rotational degrees of freedom, due to coupling between the slow relaxing, strongly adsorbed water layer at the hydrophilic oxide surface, and faster relaxation of subsequent water layers. The heterogeneity is signalled in the ruggedness of the effective free energy landscapes. We discuss possible implications of our findings in drug delivery.

Heterogeneity of dynamics in a modulated colloidal liquid

We study the dynamics of a system of two dimensional colloidal particles subjected to a spatially periodic external potential using Brownian dynamics simulations. We characterize the dynamics in the system by the mean square displacements and the self-van Hove function. The static density plots suggest that system gets into modulated liquid phase in presence of the external potential. We find that diffusion coefficients, obtained from long time mean sqaure displacements, decay exponentially with increasing potential strength. The self-van Hove functions computed from the distribution of particle displacemets in a given time interval show non-gaussian behaviour in directions both parallel and transverse to the external modulation. This suggests heterogeneous dynamics and is supported by particle mobilities and residence times.

Dynamic signature of ligand binding over a protein surface

We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.

Talazoparib in Patients with a Germline BRCA-Mutated Advanced Breast Cancer: Detailed Safety Analyses from the Phase III EMBRACA Trial

Background

In the EMBRACA phase III study (NCT01945775), talazoparib was associated with a significantly prolonged progression‐free survival (PFS) compared with physician's choice of chemotherapy (PCT) in germline BRCA1/2‐mutated HER2‐negative advanced breast cancer (ABC). Herein, the safety profile of talazoparib is explored in detail.

Materials and Methods

Overall, 412 patients received ≥1 dose of talazoparib (n = 286) or PCT (n = 126). Adverse events (AEs) were evaluated, including timing, duration, and potential overlap of selected AEs. The relationship between talazoparib plasma exposure and grade ≥3 anemia was analyzed. Time‐varying Cox proportional hazard models assessed the impact of dose reductions on PFS. Patient‐reported outcomes (PROs) in patients with common AEs and health resource utilization (HRU) were assessed in both treatment arms.

Results

The most common AEs with talazoparib were hematologic (195 [68.2%] patients) and typically occurred within the first 3–4 months of receiving talazoparib. Grade 3‐4 anemia lasted approximately 7 days for both arms. Overlapping grade 3‐4 hematologic AEs were infrequent with talazoparib. Higher talazoparib exposure was associated with grade ≥3 anemia. Permanent discontinuation of talazoparib due to hematologic AEs was low (<2%). A total of 150 (52.4%) patients receiving talazoparib had AEs associated with dose reduction. Hematologic toxicities were managed by supportive care medication (including transfusion) and dose modifications. Among patients with anemia or nausea and/or vomiting AEs, PROs favored talazoparib. After accounting for the treatment‐emergent period, talazoparib was generally associated with a lower rate of hospitalization and supportive care medication use compared with chemotherapy.

Conclusion

Talazoparib was associated with superior efficacy, favorable PROs, and lower HRU rate versus chemotherapy in gBRCA‐mutated ABC. Toxicities were manageable with talazoparib dose modification and supportive care.

Implications for Practice

Talazoparib was generally well tolerated in patients with germline BRCA‐mutated HER2‐negative advanced breast cancer in the EMBRACA trial. Common toxicities with talazoparib were primarily hematologic and infrequently resulted in permanent drug discontinuation (<2% of patients discontinued talazoparib due to hematologic toxicity). Hematologic toxicities typically occurred during the first 3–4 months of treatment and were managed by dose modifications and supportive care measures. A significant efficacy benefit, improved patient‐reported outcomes, lower rate of health resource utilization and a tolerable safety profile support incorporating talazoparib into routine management of germline BRCA‐mutated locally advanced/metastatic breast cancer.

Talazoparib is a viable option for patients with germline BRCA‐mutated advanced breast cancer. This article presents detailed safety analyses for talazoparib, as a follow‐up to reported results from the EMBRACA trial, to highlight patterns of toxicity compared with chemotherapy and to outline guidelines for management of talazoparib toxicity in clinical practice via dose modifications and/or standard supportive care.

Structural and dynamic responses of calcium ion binding loop residues in metallo-proteins

Conformational changes in bio-molecular systems are fundamental to several biological processes. It is important to study changes in responses of underlying microscopic variables, like dihedral angles as conformational change takes place. We perform all-atom simulations and modelling via Langevin equation to illustrate the changes in structural and dynamic responses of dihedral angles of calcium ion binding residues of different proteins in metal ion free (apo) and bound (holo) states. The equilibrium distributions of dihedral angles in apo- and holo-states represent structural response. Our studies show the presence of dihedrals with multiple peaks (isomeric states) separated by barrier heights is more frequent in apo- than in holo-state. The relaxation time-scale of dihedral fluctuations is found to increase linearly with decreasing barrier height due to more frequent barrier re-crossing events. The slow kinetic response of the dihedrals also contributes to slowing down of macro-scale fluctuations, which may be useful to understand kinetics of various bio-molecular processes.

In-silico studies on conformational stability of flagellin-receptor complexes

Flagellin is a protein, responsible for virulent activities of bacteria. The host cell surface receptor protein TLR5 is known to interact with flagellin in order to activate immune response. However, the underlying microscopic details of this immune response are still elusive. In this study, we report on conformational stability of flagellin of two different organisms known as fliC and flaD in bilayer with reference to water. We find that both the flagellin is conformationally more stable in bilayer than in water. We also observe that fliC-TLR5 and flaD-TLR5 complexes are conformationally stable when the extracellular domain of the protein binds to conserved D1 domain of both fliC and flaD, although the binding interface between fliC-TLR5 and flaD-TLR5 is not identical. Our studies suggest that this might lead to differences in coreceptor bindings involved in immune response and thus have potential application in pharmaceutical developments. AbbreviationsA2Aadenosine receptorDPPCdipalmitoyl phosphatidylcholineecdextracellular domainecl2extracellular loop 2eLRRextracellular Leucine rich repeat domainflaDflagellin of Vibrio choleraefliCflagellin of Salmonella typhimuriumHPVhyper-variableMDmolecular dynamicsRMSDroot means squared deviationTIRtoll-interleukin receptorTLR5toll like receptor 5VPAC1vasoactive intestinal peptide receptorCommunicated by Ramaswamy H. Sarma.

Abstract OT3-03-02: A phase 2, open-label, single-arm, multi-center study of talazoparib for neoadjuvant treatment of germline BRCA1/2 mutation patients with early-stage triple-negative breast cancer (TNBC)

Background: Approximately 15% of all breast cancers are triple negative and deleterious BRCA1/2 mutations are found in ˜11% of unselected TNBC. In the phase 3 EMBRACA trial (NCT01945775), the poly (ADP-ribose) polymerase (PARP) inhibitor talazoparib was superior to chemotherapy in prolonging progression-free survival in BRCA1/2 mutation patients with advanced breast cancer. A recent pilot study (NCT02282345) of 20 patients, explored the feasibility of neoadjuvant talazoparib in BRCA1/2 mutation patients; pathologic complete response (pCR) was reported at 53% with 6 months of single agent talazoparib.

Trial Design: This phase 2, single-arm, open-label, multi-center study has a Simon 2-stage design. Eligible pts have stage I-III invasive TNBC (ER and PR &lt;10%), with germline BRCA1/2 mutations who are suitable for neoadjuvant therapy. Pts will receive talazoparib 1 mg daily for 24 weeks, followed by breast surgery, which should occur within 4 to 6 weeks of the last dose. Ultrasound will be performed serially to assess tumor response. The primary objective is to evaluate pCR after 24 weeks of neoadjuvant talazoparib. pCR (ypT0/is ypN0) will be assessed by independent central review. Safety will also be assessed. Pts will be followed for at least 5 years to assess long term outcomes (event-free and overall survival). After surgery, any further adjuvant therapy will be given at the discretion of the treating physician. Pt reported outcomes will be assessed electronically including the global health status/quality of life, functions, and symptoms using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaires C30 and BR23. Plasma pharmacokinetic (PK) samples for determination of talazoparib concentrations will be collected at defined timepoints to describe the steady-state PK of talazoparib. Exploratory biomarker research will also take place. Approximately 122 men and women will be enrolled in the study, of which 112 evaluable pts are planned. With 112 evaluable pts and one interim futility look, the null hypothesis that the true pCR rate is 35% will be tested against a 1-sided alternative. This design yields a 1-sided type 1 error rate of 2.5% and power of 90% when the true pCR rate is 50%. An interim analysis will be performed to evaluate the efficacy of talazoparib after 28 evaluable pts undergo talazoparib treatment for 24 weeks, followed by surgery, and are assessed for pCR by central review. This trial is currently recruiting and is registered at clinicaltrials.gov (NCT03499353).

Funding: This study is sponsored by Pfizer, Inc.

Citation Format: Litton J, Symmans F, Gogineni K, Saltzman M, Telli ML, Usha L, Chakrabarti J, Tudor IC, Quek RG, Czibere A. A phase 2, open-label, single-arm, multi-center study of talazoparib for neoadjuvant treatment of germline BRCA1/2 mutation patients with early-stage triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT3-03-02.

Abstract P3-14-07: Evaluation of the effects of talazoparib on QT interval prolongation

Background: Talazoparib (TAL), an oral poly ADP-ribose polymerase inhibitor, is under investigation in multiple oncologic clinical trials and has been submitted to the US FDA for use in patients (pts) with germline BRCA-mutated, HER2-negative advanced breast cancer.

International Conference on Harmonisation guidance recommends all new drugs be evaluated for effects on cardiac repolarization in a well-controlled clinical study. For drugs for which such evaluation cannot be conducted in healthy volunteers (eg, most anticancer agents), collection of robust corrected QT (QTc) interval data from a dedicated QTc study (hybrid thorough QT/QTc study) in pts is required in the registration dossier. The effect of steady-state (ss) TAL (1 mg once daily) on cardiac repolarization in pts with advanced solid tumors was evaluated in an open-label phase 1 study (NCT03042910).

Methods: Continuous 12-lead electrocardiogram (ECG) recordings were collected at baseline (Day -1); time-matched pharmacokinetic (PK) samples and continuous ECG recordings were obtained on Days 1, 2, and 22 (when TAL concentrations achieved ss). On Day -1, pts had continuous 12-lead ECG recording starting at Time 0 (Day 1 dosing time) for 6 hrs. On Days 1 and 22, ECG recording started 45 min before TAL administration and continued for 6 hrs post dose and blood samples for PK were collected before dose and at 1, 2, 4, and 6 hrs post dose. On Day 2, a 30-min ECG recording and a PK sample were obtained before dose at Time 0.

Continuous ECG recordings were submitted to a central laboratory; triplicate 10-sec ECGs were extracted from a 5-min extraction window beginning 15 min before each PK collection time. ECG measurements were reported via blinded manual adjudication process and included PR interval, QT interval, RR interval, and QRS complex. The QT interval was corrected for effect of heart rate using Fridericia's correction (QTcF) and Bazett's correction (QTcB).

The estimate of change from time-matched baseline and its 2-sided 90% confidence interval (CI) was calculated for each nominal time point using PROC MEANS. Additionally, a prespecified PK/pharmacodynamic (PD) model was used to describe the relationship between plasma TAL concentrations ([TAL]) and QTc. The prespecified linear mixed-effects model included [TAL], time (categorical), and treatment with random pt effects on [TAL] and the intercept. If the upper bounds (UB) of 1-sided 95% CIs of time-matched ΔQTc for all ECG time points were &lt;20 msec and the UB of 1-sided 95% CIs of the predicted ΔQTc at the mean ss maximum [TAL] was &lt;20 msec, the effect of TAL on QTc was not of clinical relevance.

Results: 37 of 38 pts enrolled received TAL and were included in the ECG and PK/PD analyses. No pts had a postbaseline absolute maximum QTcF or QTcB ≥500 msec or ΔQTc ≥60 msec. The UB of the 1-sided 95% CI for the time-matched ΔQTcF and ΔQTcB were &lt;12 msec at all nominal ECG time points. In the PK/PD analysis, the slopes (95% CI) of QTcF-[TAL] and QTcB-[TAL] relationships were -0.14 (-0.78 to 0.50) msec/ng/mL and -0.24 (-0.88 to 0.41) msec/ng/mL, respectively, indicating that TAL did not have a concentration-dependent effect on QTcF or QTcB.

Conclusion: TAL does not have a clinically relevant effect on QTc.

Funding: Medivation LLC, acquired by Pfizer.

Citation Format: Hoffman J, Chakrabarti J, Wainberg ZA, Plotka A, Babu S, Milillo Naraine A, Kanamori D, Moroose R, Nguyen L, Wang D. Evaluation of the effects of talazoparib on QT interval prolongation [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-14-07.

Transient dynamical responses of a charged binary colloid in an electric field

In a model system of oppositely charged colloids we study via Brownian dynamics simulation the dynamical response as the system approaches steady states upon application of a constant electric field. The system is known to form patterns of like charges in the transverse plane to the field that are elongated along the field as lanes. We show that an increase in structural heterogeneity leads to non-Gaussian tails in the probability distribution of particle displacements [self van Hove functions (self-vHfs)]. The self-diffusion coefficient depends upon the time of the observations and consequently indicates aging in the system. However, the anomalies in the self-vHfs and diffusion do not appear during the melting of the structures.

Evaluation of hepatic impairment on pharmacokinetics and safety of crizotinib in patients with advanced cancer

PURPOSE

This phase 1 study evaluated the effect of hepatic impairment on pharmacokinetics and safety of crizotinib in patients with advanced cancer.

METHODS

Patients were dosed according to hepatic function classified by modified National Cancer Institute Organ Dysfunction Working Group criteria and group assignment [normal (A1 and A2), mild (B), moderate (C1 and C2), or severe (D)]. Primary pharmacokinetic endpoints included area under the concentration-time curve as daily exposure (AUC_daily) and maximum plasma concentration (C_max) at steady state. Safety endpoints included types, incidence, seriousness, and relationship to crizotinib of adverse events.

RESULTS

The AUC_daily and C_max in patients with normal liver function were 7107 ng h/mL and 375.1 ng/mL (A1) and 5422 ng h/mL and 283.9 ng/mL (A2), respectively. The AUC_daily and C_max ratios of adjusted geometric means for Groups B, C2, and D versus Group A1 were 91.12 and 91.20, 114.08 and 108.87, and 64.47 and 72.63, respectively. Any grade treatment-related adverse events (TRAEs) occurred in 75% of patients; grade 3/4 TRAEs occurred in 25%, including fatigue (6%), hyponatremia (5%), and hyperbilirubinemia (3%).

CONCLUSIONS

No adjustment to the approved 250 mg twice daily (BID) dose of crizotinib is recommended for patients with mild hepatic impairment. The recommended dose is 200 mg BID for patients with moderate hepatic impairment, and the dose should not exceed 250 mg daily for patients with severe hepatic impairment. Adverse events appeared consistent among the hepatic impairment groups.

CLINICAL TRIAL REGISTRATION NO

NCT01576406.

Static and dynamic properties of two-dimensional Coulomb clusters

We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional confinements across the crossover from solid- to liquid-like behaviors. While static correlations that investigate the translational and bond orientational order in the confinements show the footprints of hexatic-like phase at low temperatures, dynamics of the particles slow down considerably in this phase, reminiscent of a supercooled liquid. Using density correlations, we probe long-lived heterogeneities arising from the interplay of the irregularity in the confinement and long-range Coulomb interactions. The relaxation at multiple time scales show stretched-exponential decay of spatial correlations in irregular traps. Temperature dependence of characteristic time scales, depicting the structural relaxation of the system, show striking similarities with those observed for the glassy systems, indicating that some of the key signatures of supercooled liquids emerge in confinements with lower spatial symmetries.

Allostery in Orai1 binding to calmodulin revealed from conformational thermodynamics

Here, we study microscopic mechanism of complex formation between Ca²⁺-bound calmodulin (holoCaM) and Orai1 that regulates Ca²⁺-dependent inactivation process in eukaryotic cells. We compute conformational thermodynamic changes in holoCaM with respect to complex of Orai1 bound to C-terminal domain of holoCaM using histograms of dihedral angles of the proteins over trajectories from molecular dynamics simulations. Our analysis shows that the N-terminal domain residues L4, T5, Q41, N42, T44 and E67 of holoCaM get destabilized and disordered due to Orai1 binding to C-terminal domain of calmodulin affect the N-terminal domain residues. Among these residues, polar T44, having maximum destabilization and disorder via backbone fluctuations, shows the largest change in solvent exposure. This suggests that N-terminal domain is allosterically regulated via T44 by the binding of Orai1 to the C-terminal domain.

Molecular dynamics studies on conformational thermodynamics of Orai1-calmodulin complex

Molecular understanding of bio-macromolecular binding is a challenging task due to large sizes of the molecules and presence of variety of interactions. Here, we study the molecular mechanism of calmodulin (CaM) binding to Orai1 that regulates Ca²⁺-dependent inactivation process in eukaryotic cells. Although experimental observations indicate that Orai1 binds to the C-terminal of Ca²⁺-loaded CaM, it is not decisive if N-domain of CaM interacts with Orai1. We address the issue of interaction of different domains of CaM with Orai1 using conformational thermodynamic changes, computed from histograms of dihedral angles over simulated trajectories of CaM, CaM-binding domain of Orai1 and complexes of CaM with Orai1. The changes for all residues of both C and N terminal domains of CaM upon Orai1 binding are compared. Our analysis shows that Orai1binds to both C-terminal and N-terminal domains of CaM, indicating 1:2 stoichiometry. The Orai1 binding to N-terminal domain of CaM is less stable than that to the C-terminal domain. The binding residues are primarily hydrophobic. These observations are in qualitative agreement to the experiments. The conformational thermodynamic changes thus provide a useful computational tool to provide atomic details of interactions in bio-macromolecular binding.

Safety and pharmacokinetics of crizotinib in patients (pts) with hepatic impairment (HI) and advanced cancer

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Background: Crizotinib is a kinase inhibitor approved for treating ALK+ and ROS1+ advanced non-small cell lung cancer. Since crizotinib undergoes hepatic metabolism, this phase 1 study evaluated the pharmacokinetics (PK) and safety of crizotinib in pts with liver dysfunction. Methods: Crizotinib-naïve pts with different types of advanced cancer (ALK and ROS1 status unknown), ≥ 18 yr old, and ECOG PS 0–2 were enrolled. Pts were assigned to groups A1 – D based on liver function: normal (A1/A2) = both AST and TB ≤ the upper limit of normal (ULN); mild impairment (B) = AST > ULN and TB ≤ ULN, or TB > 1.0 – 1.5 × ULN; moderate (C1/C2) = TB > 1.5 – 3 × ULN; severe (D) = TB > 3 × ULN. Starting dose was based on HI. Pts in A1 and A2 were matched for weight, age, gender, race and ECOG PS to pts in B and C2, respectively. Study objectives included PK, safety and antitumor activity. Results: 88 pts were enrolled in A1 (n=11), A2 (n=15), B (n=20), C1 (n=10), C2 (n=16) and D (n=16). The geometric means of PK parameters at steady-state (Cycle 2 Day 1) are shown below. 75% of pts experienced treatment-related AEs (TRAEs), 9 (81.8%), 14 (93.3%), 15 (75.0%), 6 (60.0%), 11 (68.8%) and 11 (68.8%) in groups A1, A2, B, C1, C2 and D, respectively. 25% of pts experienced Grade 3/4 TRAEs, 3 (27.3%), 3 (20.0%), 3 (15.0%), 1 (10%), 7 (43.8%), 5 (31.3%) in groups A1, A2, B, C1, C2 and D, respectively. Three (3.4%) pts, all in A2, experienced treatment-related SAEs. Two pts (10%) in B and 1 (6.3%) in C2 required dose reductions for TRAEs. TRAEs associated with permanent discontinuation of treatment occurred in 1 pt in A1, A2, C2 and D. Overall, 3 pts had partial responses with durations of 96, 17 and 17 wks; 25 pts had stable disease. Conclusions: Systemic exposures of crizotinib in pts with mild HI receiving 250 BID and in pts with moderate HI receiving 200 mg BID are comparable with that of pts with normal hepatic function at 250 mg BID. All TRAEs were manageable across the various levels of hepatic function. Clinical trial information: NCT01576406. [Table: see text]

Conformational thermodynamics guided structural reconstruction of biomolecular fragments

Conformational thermodynamics compares the modeling protocols to identify the conformation of the missing region leading to a suitable model for metal ion free (apo) skeletal muscle Troponin C.

Quantum chemical studies on nucleophilic sites in calcium ion bound zwitterionic calmodulin loops

Quantum chemical calculation on Ca²⁺ bound zwitterionic calmodulin-loops shows terminal capping contributions localized near HOMO and LUMO, which decay exponentially and presence of nucleophilic site at the phenyl-ring O_h of Y99.

Quantum Chemical Studies on Stability and Chemical Activities in Calcium Ion Bound Calmodulin Loops

Quantum chemical (QC) calculations for macromolecules require truncation of the molecule, highlighting the portion of interest due to heavy computation cost. As a result, an estimation of the effects of truncation is important to interpret the energy spectrum of such calculations. We perform density functional theory based QC calculations on calcium ion bound EF-hand loops of Calmodulin isolated from the crystal structure in an implicit solvent. We find that the terminal contributions of neutral capping are negligible across the entire ground-state energy spectrum. The coordination energy range and the nature of hybridization of the coordination state molecular orbitals remain qualitatively similar across these loops. While the HOMO and LUMO of loops in the N-terminal domain are dominated by the acidic aspartates, and the polar/hydrophobic residues, respectively, these levels of the C-terminal domain loops show strong localized electron density on the phenyl rings of the tyrosines. The Fukui index calculation identifies the hydroxyl oxygen in the phenyl ring of Y99 as a potent nucleophile. Our analysis indicates a general way of interpreting the electronic energy spectra to understand stability and functions of large biomolecules where the truncation of the molecule and, hence, the terminal capping effects are inevitable.

A microscopic insight from conformational thermodynamics to functional ligand binding in proteins

We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca(2+)-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca(2+)-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg(2+)-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca(2+)-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg(2+)-aLA are few, and hence, the oleic acid binding to Mg(2+)-bound aLA is less stable than that to the Ca(2+)-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins.

Cross-over between central and non-central conservative effective forces in a modulated colloidal fluid

We study by Monte Carlo simulations the effective forces between two particles dispersed in a two-dimensional colloidal fluid, modulated in one direction by a spatially periodic external potential. When the modulation strength exceeds the strength of interaction between the dispersed and dispersing particles, the anisotropic effective forces, show cross-over between central and non-central nature, although the effective forces remain conservative. The non-central nature of the effective forces depends on the orientation of the separation vector between the dispersed particles with respect to the modulation direction.

Serum leptin level in women with polycystic ovary syndrome: correlation with adiposity, insulin, and circulating testosterone

BACKGROUND

Leptin, an adipocyte-derived hormone encoded by 'ob' gene, serves as a link relaying metabolic signals to the neuronal networks in the brain to modulate hypothalamo-pituitary-ovarian axis. Circulating leptin correlates strongly with obesity, which is frequently associated with polycystic ovarian syndrome (PCOS), a major form of dysovulatory infertility in women, characterized by endocrine abnormalities such as hyperandrogenism and inappropriate LH secretion. PCOS is also often associated with insulin resistance and hyperinsulinemia, features that are linked to leptin and its receptors. However, the relationship between leptin and gonadotropins, androgens, and insulin in PCOS is still controversial.

AIM

Present investigation attempts to evaluate the interrelationship between serum leptin level with body mass index, insulin and with circulating testosterone in PCOS women.

SUBJECTS AND METHODS

Women diagnosed with either tubal block/male factor infertility (Control; n = 18) and with PCOS (n = 16), enrolled for in vitro fertilization and embryo transfer (IVF-ET), were recruited for this study. All were reviewed for body mass index (BMI), endocrine milieu (including pituitary gonadotropins, TSH, prolactin, gonadal steroids, and insulin) and for circulating serum leptin. Interpretation of data was done using PRISM Statistical Software Package (PRISM Version 4.03@1992-2005; GraphPad Software Inc).

RESULTS

Positive correlation was observed between serum leptin, BMI, and insulin in both the groups. Mean BMI, LH, and LH: FSH ratios were found elevated in the PCOS population. PCOS women also had significantly elevated androgens and fasting levels of insulin.

CONCLUSION

Hyperleptinemia in PCOS women appears to be due to the positive correlation between serum leptin, BMI, and insulin.

Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.

Dimensional crossover in fluids under nanometer-scale confinement

Several earlier studies have shown signatures of crossover in various static and dynamics properties of a confined fluid when the confining dimension decreases to about a nanometer. The density fluctuations govern the majority of such properties of a fluid. Here, we illustrate the crossover in density fluctuation in a confined fluid, to provide a generic understanding of confinement-induced crossover of fluid properties, using computer simulations. The crossover can be understood as a manifestation of changes in the long-wavelength behavior of fluctuation in density due to geometrical constraints. We further show that the confining potential significantly affects the crossover behavior.

High-affinity quasi-specific sites in the genome: how the DNA-binding proteins cope with them

Many prokaryotic transcription factors home in on one or a few target sites in the presence of a huge number of nonspecific sites. Our analysis of λ-repressor in the Escherichia coli genome based on single basepair substitution experiments shows the presence of hundreds of sites having binding energy within 3 Kcal/mole of the O(R)1 binding energy, and thousands of sites with binding energy above the nonspecific binding energy. The effect of such sites on DNA-based processes has not been fully explored. The presence of such sites dramatically lowers the occupation probability of the specific site far more than if the genome were composed of nonspecific sites only. Our Brownian dynamics studies show that the presence of quasi-specific sites results in very significant kinetic effects as well. In contrast to λ-repressor, the E. coli genome has orders of magnitude lower quasi-specific sites for GalR, an integral transcription factor, thus causing little competition for the specific site. We propose that GalR and perhaps repressors of the same family have evolved binding modes that lead to much smaller numbers of quasi-specific sites to remove the untoward effects of genomic DNA.

Gold nanoparticle superlattices as functional solids for concomitant conductivity and SERS tuning

Mercaptosuccinic acid protected gold nanoparticles (Au@MSA) self assemble to form superlattice (SL) crystals at the air-water interface. These have been used for gas adsorption. The current-voltage (I-V) characteristics of the SL film with embedded SL crystals, obtained by four probe measurements, show Ohmic conduction. The conductance observed was proportional to the polarizability of the adsorbed gases. The current through the SL decreases on adsorption of the gas along with decrease in the SERS intensity of a probe molecule from the crystals. We rationalise our observation of the linear dependence of the conductance on the polarizability of the adsorbed gas using a simple model calculation. Variation of the conductance may be useful in designing electrical switches operating at the nanometre length scales.