Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors

Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.

Comparison of sequential versus simultaneous integrated boost of volumetric modulated arc therapy in treatment of oropharyngeal carcinoma

OBJECTIVE

Volumetric modulated arc therapy (VMAT) is a useful treatment technique that can reduce treatment time while producing improved dose distribution to target structures. The main aim of the study is to evaluate the outcome of oropharyngeal cancer patients treated with VMAT, sequential (SEQ) versus simultaneous integrated boost (SIB) technique in terms of survival and failures and to assess late radiation toxicities with their dosimetric parameters.

MATERIAL AND METHODS

Total 54 patients of histologically proved oropharyngeal cancer patients treated by definitive radiotherapy using VMAT technique in January 2019 to December 2020 were followed up and evaluated in terms of survival, patterns of failure and late radiation toxicities by RTOG toxicity criteria.

RESULTS

After a median follow up of 12 months, overall survival (OS) and disease free survival (DFS) were 64.8% and 48.1% respectively. In terms of patterns of failure, 44.4% showed local recurrence, 7.4% as regional relapse and 3.7% showed distant metastasis. While comparing sequential versus SIB, no significant difference was found in OS (64.9% vs. 59.8%, p = 0.689), DFS (52.8% vs. 35.3%, p = 0.266), local control (LC) (58.3% vs. 47.1%, p = 0.437) and regional control (RC) (94.3% vs. 88.2%, p = 0.151) respectively. Among late radiation toxicities, the most common were xerostomia (42.2% for SEQ and 24.2% for SIB group), dysphagia (33.3% for SEQ and 15.1% for SIB group) and hoarseness of voice (15.1% for SEQ and 12.1% for SIB group).

CONCLUSION

SIB technique proved better than SEQ technique in terms of pattern of failure or late toxicity, but no significant difference can be reported.

Critical Appraisal of Paediatric Embryonal Cancers Treated with Image-guided Intensity-modulated Proton Therapy

AIM

To carry out a comprehensive critical appraisal of image-guided intensity-modulated proton therapy practice for craniospinal irradiation (CSI).

MATERIALS AND METHODS

An image-guided intensity-modulated proton therapy database of 45 consecutive paediatric patients with central nervous system embryonal malignancies treated between January 2019 and April 2022 were critically appraised for demography, diagnosis, treatment planning strategy and treatment delivery accuracy.

RESULTS

Most patients (median age: 7.5 years; male:female ratio: 34:11) had medulloblastoma (56%), followed by recurrent ependymoma (19%), pinealoblastoma (5%), germ cell (5%) and others (15%). The dose to the planning target volume-craniospinal (PTV-CS; length 39.06-79.59 cm) varied from 21 to 35 GyRBE, whereas the combined median dose to craniospinal and boost was 54 GyRBE. In all patients, the 95% isodose line covered the cribriform plate completely and optic nerves mostly, with a median V95% of 100% and 82.96%, keeping Dmax to the lens <3.9 GyRBE. In skeletally immature patients (88.38%), the anterior vertebral body was completely covered in 18.18% and underdosed in 70.15% of the cases, resulting in a median Dmean of 10.11 GyRBE to the oesophagus. Lateral spine coverage was maintained on the edges of the vertebral body in 52.2%, whereas it extended beyond in 48.8%. The median V98% for clinical target volumes and V95% for PTVs of the brain, spine and craniospinal were >97%, with excellent conformity (0.89) and homogeneity (0.07) indices for PTV-CS. All neurological organs at risk received a median Dmax ranging from 36 to 44 GyRBE from the combined CSI and boost regimens. Analysis of patient-specific quality assurance results revealed that 545 (97.67%) planar dosage verification had gamma (3% at 3 mm) values >95%. The online patient set-up verification showed translational and rotational deviation within 2 mm and 0.5° in 88-94% and 97% of the cases. Systematic and random error were within 0.90 mm and 1.71 mm in translation and 0.1° and 0.2° in rotation.

CONCLUSION

A change in practice pattern was observed. The findings from our comprehensive critical appraisal add to the growing library of CSI practice and may serve as a reference for inter-institutional comparison.

A dosemetric and radiobiological impact of VMAT and 3DCRT on lumbosacral plexuses, an underestimated organ at risk in cervical cancer patients

Background

The purpose of this study was to evaluate dosimetric and radiobiological difference between volumetric modulated arc therapy (VMAT) and 3-dimensional conformal radiotherapy (3DCRT) in organ at risk (OAR) lumbosacral plexus (LSP) in cervical cancer patients.

Materials and methods

30 patients of cervical cancer who were treated using 3DCRT or VMAT along with chemotherapy followed by brachytherapy were enrolled. LSP was delineated retrospectively. Dosimetric and radiobiological difference was evaluated. Patients were followed for radiation induced lumbosacral plexopathy (RILSP).

Results

Median follow-up was 12 months (3–16 months). 53.3% of patients were treated by 3DCRT and 46.7% by VMAT. The mean (±SD) LSP volume: 119.03 ± 15 cm³. The mean volume percentages (%) of the LSP: V5, V10, V20, V30, V40, V50, V55, and V60 were 100%, 99.8%, 99.2%, 94.3%, 84.03%, 59.7%, 0%, 0%, respectively. All patients received doses to the LSP in excess of 50 Gy, one patient received 55 Gy. A statistically significant difference was observed in the median value of V20, V30, V40, V50, D50, P2, P4, P7, P8, P9, and P10 across two different techniques of radiotherapy — VMAT and 3DCRT. None of the patients presented with RILSP. NTCP value was less in VMAT plans compared to 3DCRT, which is also statistically significant.

Conclusion

RILSP is a rare and often refractory complication of pelvic radiotherapy. Advance radiotherapy technique with proper OAR delineation and constraint can prevent the occurrence of RILSP. VMAT has potential benefits for the probability of dose reduction in LSP. Further studies are required focusing on dose distribution in LSP–OAR and radiotherapy modality.

Insight into the structural requirements of gelatinases (MMP-2 and MMP-9) inhibitors by multiple validated molecular modelling approaches: Part II

Inhibition of the matrix metalloproteinases (MMPs) is effective against metastasis of secondary tumours. Previous MMP inhibitors have failed in clinical trials due to their off-target toxicity in solid tumours. Thus, newer MMP inhibitors now have paramount importance. Here, different molecular modelling techniques were applied on a dataset of 110 gelatinase (MMP-2 and MMP-9) inhibitors. The objectives of the present study were to identify structural fingerprints for gelatinase inhibition and also to develop statistically validated QSAR models for the screening and prediction of different derivatives as MMP-2 (gelatinase A) and MMP-9 (gelatinase B) inhibitors. The Bayesian classification study provided the ROC values for the training set of 0.837 and 0.815 for MMP-2 and MMP-9, respectively. The linear model also produced the leave-one-out cross-validated Q² of 0.805 (eq. 1, MMP-2) and 0.724 (eq. 2, MMP-9), an r² of 0.845 (eq. 1, MMP-2) and 0.782 (eq. 2, MMP-9), an r²_Pred of 0.806 (eq. 1, MMP-2) and 0.732 (eq. 2, MMP-9). Similarly, non-linear learning models were also statistically significant and reliable. Overall, this study may help in the rational design of newer compounds with higher gelatinase inhibition to fight against both primary and secondary cancers in future.

First molecular modelling report on tri-substituted pyrazolines as phosphodiesterase 5 (PDE5) inhibitors through classical and machine learning based multi-QSAR analysis

Phosphodiesterase 5 (PDE5) falls under a broad category of metallohydrolase enzymes responsible for the catalysis of the phosphodiesterase bond, and thus it can terminate the action of cyclic guanosine monophosphate (cGMP). Overexpression of this enzyme leads to development of a number of pathological conditions. Thus, targeting the enzyme to develop inhibitors could be useful for the treatment of erectile dysfunction as well as pulmonary hypertension. In the current study, several molecular modelling techniques were utilized including Bayesian classification, single tree and forest tree recursive partitioning, and genetic function approximation to identify crucial structural fingerprints important for optimization of tri-substituted pyrazoline derivatives as PDE5 inhibitors. Later, various machine learning models were also developed that could be utilized to predict and screen PDE5 inhibitors in the future.

Infection Control and Modified Workflow Strategies in Radiation Oncology Department during COVID 19 Crisis: An Institutional Experience

Purpose: To build safe environment for cancer fighters and radiation personnel during COVID-19 pandemic by focusing on infection control, workflow and radiotherapy dose schedules modification strategies in radiation oncology departments. Material and Methods: A meeting was called post lock down in radiation oncology department to prepare infection control policies and workflow strategies in time of COVID-19 Pandemic.Results: Strategies and policies were formed during COVID-19 crises taking following points into consideration 1) Infection control policies 2) CT simulation policies 3) Day care admission and chemotherapy administration policies 4) Radiation treatment plan modification and delivery strategies 5) Brachytherapy delivery strategies.Conclusion: Management of cancer patients is an issue running parallel to the present condition of COVID-19 pandemic. Further randomized trial on hypofractionated radiotherapy schedules should be encouraged. Positivity, awareness and systematic approach are most important step in balancing the current scenario.

Autosomal Clonal Monoallelic Expression: Natural or Artifactual?

The prevalence of mitotically heritable clonal random monoallelic expression of autosomal genes (aRME) remains controversial. Specifically, presence of clonal aRME is well supported in vitro but remains elusive in vivo. Here, we provide critical insights into this matter and discuss whether prevalent clonal aRME is natural or artifactual.

Geospatial Distribution and Predictors of Mortality in Hospitalized Patients With COVID-19: A Cohort Study

BACKGROUND

The global coronavirus disease 2019 (COVID-19) pandemic offers the opportunity to assess how hospitals manage the care of hospitalized patients with varying demographics and clinical presentations. The goal of this study was to demonstrate the impact of densely populated residential areas on hospitalization and to identify predictors of length of stay and mortality in hospitalized patients with COVID-19 in one of the hardest hit counties internationally.

METHODS

This was a single-center cohort study of 1325 sequentially hospitalized patients with COVID-19 in New York between March 2, 2020, to May 11, 2020. Geospatial distribution of study patients' residences relative to population density in the region were mapped, and data analysis included hospital length of stay, need and duration of invasive mechanical ventilation (IMV), and mortality. Logistic regression models were constructed to predict discharge dispositions in the remaining active study patients.

RESULTS

The median age of the study cohort (interquartile range [IQR]) was 62 (49-75) years, and more than half were male (57%) with history of hypertension (60%), obesity (41%), and diabetes (42%). Geographic residence of the study patients was disproportionately associated with areas of higher population density (r s = 0.235; P = .004), with noted "hot spots" in the region. Study patients were predominantly hypertensive (MAP > 90 mmHg; 670, 51%) on presentation with lymphopenia (590, 55%), hyponatremia (411, 31%), and kidney dysfunction (estimated glomerular filtration rate < 60 mL/min/1.73 m2; 381, 29%). Of the patients with a disposition (1188/1325), 15% (182/1188) required IMV and 21% (250/1188) developed acute kidney injury. In patients on IMV, the median (IQR) hospital length of stay in survivors (22 [16.5-29.5] days) was significantly longer than that of nonsurvivors (15 [10-23.75] days), but this was not due to prolonged time on the ventilator. The overall mortality in all hospitalized patients was 15%, and in patients receiving IMV it was 48%, which is predicted to minimally rise from 48% to 49% based on logistic regression models constructed to project disposition in the remaining patients on ventilators. Acute kidney injury during hospitalization (odds ratioE, 3.23) was the strongest predictor of mortality in patients requiring IMV.

CONCLUSIONS

This is the first study to collectively utilize the demographics, clinical characteristics, and hospital course of COVID-19 patients to identify predictors of poor outcomes that can be used for resource allocation in future waves of the pandemic.

Adjuvant Irradiation in Carcinoma Breast Patients: Comparison of 3DCRT and Semi-automated Complex VMAT Hypofractionated Plans

OBJECTIVE

Adjuvant radiotherapy is required for most post MRM breast cancer patients. Aim of treatment is to target radiation to region of interest while sparing Organs at Risk (OARs). Attempts are being made to decrease dose to OARs without compromising target coverage by evolving radiation techniques. In this study, a comparison of traditional 3DCRT plans is done with semi-automated complex VMAT plans for dose received by OARs namely Contralateral Breast (CLB), Ipsilateral lung (I/LL), and Contralateral Lung (C/LL).

MATERIALS AND METHODS

It was planned for 30 post MRM breast cancer patients for chest wall, ipsilateral axilla and supraclavicular lymph node. The PTV dose was 42.5 Gy in 16 fractions, 2.66 Gy/fraction, 5 days a week. For each patient traditional 3DCRT and semi-automated complex VMAT plans (conventional + tangential VMAT plans) were prepared and evaluated by radiation oncologists.

RESULTS

Dose evaluation of CLB shows higher Dmax for 3DCRT plans, while, Dmean was lower for the 3DCRT plan. Difference between D2 was not significant. V2.5 was significantly less in 3DCRT, while, difference between V5 and V10 were not significant. For C/LL Dmean, V2.5, V5, and V10 were higher for the VMAT plan. For I/LL Dmean, V5 and V10 were higher, while V20 and V30 were lower for VMAT plans.

DISCUSSION AND CONCLUSION

The VMAT technique described here is a useful treatment option available for difficult planning situations. OARs stated above had a mixed result showing VMAT plans to be inferior at lower dose metrics, while, superior at higher dose metrics.

Identification of structural fingerprints for ABCG2 inhibition by using Monte Carlo optimization, Bayesian classification, and structural and physicochemical interpretation (SPCI) analysis

The human breast cancer resistance protein (BCRP), one of the members of the large ATP binding cassette (ABC) transporter superfamily, is crucial for resistance against chemotherapeutic agents. Currently, it has been emerged as one of the best biological targets for the designing of small molecule drugs capable of eliminating multidrug resistance in breast cancer. In order to gain insights into the relationship between the molecular structure of compounds and the ABCG2 inhibition, a multi-QSAR approach using different methods was performed on a dataset of 294 ABCG2 inhibitors with diverse scaffolds. The best models obtained by different chemometric methods have the following statistical characteristics: Monte Carlo Optimization-based QSAR (sensitivity = 0.905, specificity = 0.6255, accuracy = 0.756, and MCC = 0.545), Bayesian classification model (sensitivity = 0.735, specificity = 0.775, and concordance = 0.757); structural and physicochemical interpretation analysis-random forest method (balance accuracy = 0.750, sensitivity = 0.810, and specificity = 0.700). Additionally, structural fingerprints modulating the ABCG2 inhibitory properties were identified from the best models of each method and also validated with each other. The current modelling study is an attempt to get a deep insight into the different important structural fingerprints modulating ABCG2 inhibition.

Dosimetric comparison of coplanar and non-coplanar volumetric-modulated arc therapy in head and neck cancer treated with radiotherapy

Purpose

To evaluate the dosimetric variations in patients of head and neck cancer treated with definitive or adjuvant radiotherapy using optimized non-coplanar (ncVMAT) beams with coplanar (cVMAT) beams using volumetric arc therapy.

Materials and Methods

Twenty-two patients of head and neck cancer that had received radiotherapy using VMAT in our department were retrospectively analyzed. Each of the patients was planned using coplanar and non-coplanar orientations using an optimized couch angle and fluences. We analyzed the Conformity Index (CI_RTOG), Dose Homogeneity Index (DHI), Heterogeneity Index (HI_RTOG), low dose volume, target and organs-at-risk coverage in both the plans without changing planning optimization parameters.

Results

The prescription dose ranged from 60 Gy to 70 Gy. Using ncVMAT, CI_RTOG, DHI and HI_RTOG, and tumor coverage (ID_95%) had improved, low dose spillage volume in the body V_5Gy was increased and V_10Gy was reduced. Integral dose and intensity-modulated radiation therapy factor had increased in ncVMAT. In the case of non-coplanar beam arrangements, maximum dose (D_max) of right and left humeral head were reduced significantly whereas apex of the right and left lung mean dose were increased.

Conclusion

The use of ncVMAT produced better target coverage and sparing of the shoulder and soft tissue of the neck as well as the critical organ compared with the cVMAT in patients of head and neck malignancy.

Insight into structural features of phenyltetrazole derivatives as ABCG2 inhibitors for the treatment of multidrug resistance in cancer

ABCG2 is the principal ABC transporter involved in the multidrug resistance of breast cancer. Looking at the current demand in the development of ABCG2 inhibitors for the treatment of multidrug-resistant cancer, we have explored structural requirements of phenyltetrazole derivatives for ABCG2 inhibition by combining classical QSAR, Bayesian classification modelling and molecular docking studies. For classical QSAR, structural descriptors were calculated from the free software tool PaDEL-descriptor. Stepwise multiple linear regression (SMLR) was used for model generation. A statistically significant model was generated and validated with different parameters (For training set: r = 0.825; Q² = 0.570 and for test set: r = 0.894, r²_pred = 0.783). The predicted model was found to satisfy the Golbraikh and Trospha criteria for model acceptability. Bayesian classification modelling was also performed (ROC scores were 0.722 and 0.767 for the training and test sets, respectively). Finally, the binding interactions of phenyltetrazole type inhibitor with the ABCG2 receptor were mapped with the help of molecular docking study. The result of the docking analysis is aligned with the classical QSAR and Bayesian classification studies. The combined modelling study will guide the medicinal chemists to act faster in the drug discovery of ABCG2 inhibitors for the management of resistant breast cancer.

Structural exploration of hydroxyethylamines as HIV-1 protease inhibitors: new features identified

The current study deals with chemometric modelling strategies (Naïve Bayes classification, hologram-based quantitative structure-activity relationship (HQSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)) to explore the important features of hydroxylamine derivatives for exerting potent human immunodeficiency virus-1 (HIV-1) protease inhibition. Depending on the statistically validated reliable and robust quantitative structure-activity relationship (QSAR) models, important and crucial structural features have been identified that may be responsible for enhancing the activity profile of these hydroxylamine compounds. Arylsulfonamide function along with methoxy or fluoro substitution is important for enhancing activity. Bulky steric substitution at the sulfonamide nitrogen disfavours activity whereas smaller hydrophobic substitution at the same position is found to be favourable. Apart from the crucial oxazolidinone moiety, pyrrolidine, cyclic urea and methyl ester functions are also responsible for increasing the HIV-1 protease inhibitory profile. Observations derived from these modelling studies may be utilized further in designing promising HIV-1 protease inhibitors of this class.

Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization

Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors. The best models from different splits were selected on the basis of statistically validated characteristics of the test set and have the following statistical parameters: r² = 0.806, Q² = 0.788 (split 1); r² = 0.842, Q² = 0.826 (split 2); r² = 0.774, Q² = 0.755 (split 3). The structural attributes obtained from the best models were analysed to understand the structural requirements of the selected series for HIV-1 protease inhibitory activity. On the basis of obtained structural attributes, 11 new compounds were designed, out of which five compounds were found to have better activity than the best active compound in the series.

Insight into the structural requirements of pyrimidine-based phosphodiesterase 10A (PDE10A) inhibitors by multiple validated 3D QSAR approaches

Schizophrenia is a complex disorder of thinking and behaviour (0.3-0.7% of the population is affected). The over-expression of phosphodiesterase 10A (PDE10A) enzyme may be a potential target for schizophrenia and Huntington's disease. Because 3D QSAR analysis is one of the most frequently used modelling techniques, in the present study, five different 3D QSAR tools, namely CoMFA, CoMSIA, kNN-MFA, Open3DQSAR and topomer CoMFA methods, were used on a dataset of pyrimidine-based PDE10A inhibitors. All developed models were validated internally and externally. The non-commercial Open3DQSAR produced the best statistical results amongst 3D QSAR tools. The structural interpretations obtained from different methods were thoroughly analysed and were justified on the basis of information obtained from the crystal structure. Information from one method was mostly validated by the results of other methods and vice versa. In the current work, the use of multiple tools in the same analysis revealed more complete information about the structural requirements of these compounds. On the basis of the observations of the 3D QSAR studies, 12 new compounds were designed for better PDE10A inhibitory activity. The current investigation may help in further designing new PDE10A inhibitors with promising activity.

Greek Warrior Helmet Facies (Wolf-hirschhorn Syndrome)

Wolf-Hirschhorn syndrome (WHS) is caused by a chromosomal deletion of the band 4p16.3 with characteristic craniofacial features -’Greek warrior helmet’5 facies (prominent glabella, hypertelorism, broad beaked nose and frontal bossing), high-arched eyebrows, protruding eyes, epicanthal folds, short philtrum, distinct mouth with downturned corners, micrognathia, dysplastic ears, preauricular tags. Till date there are very few case reports of Wolf-Hirschhorn syndrome.Here we report a case that had characteristic dysmorphic facies (Figure 1) ‘Greek warrior helmet’ and was diagnosed as a case of WHS. But presence of Meningo-encephalocele and lissencephaly is rarely reported in literature in association with Wolf-hirschhorn syndrome till date. J Nepal Paediatr Soc 2014;34(3):239-243 DOI: http://dx.doi.org/10.3126/jnps.v34i3.10289

Time-resolved ring structure of circularly polarized beams backscattered from forward scattering media

The backscattering of circularly polarized light at normal incidence to a half-space of scattering particles is studied using the Electric Field Monte Carlo (EMC) method. The spatial distribution of the backscattered light intensity is examined for both the time-resolved and continuous wave cases for large particles with anisotropy factor, g, in the range 0.8 to 0.97. For the time-resolved case, the backscattered light with the same helicity as that of the incident beam (co-polarized) is found to form a ring centered on the point of incidence. The ring expands and simultaneously grows weak as time increases. The intensity of backscattered light with helicity opposite to that of the incident beam (cross-polarized) is found to exhibit a ring behavior for g >/= 0.85, with significant backscattering at the point of incidence. For the continuous-wave case no such ring pattern is observed in backscattered light for either helicity. The present EMC study suggests that the ring behavior can only be observed in the time domain, in contrast to previous studies of light backscattered from forward scattering media based on the scalar time-independent Fokker-Planck approximation to the radiative transfer equation. The time-dependent ring structure of backscattered light may have potential use in subsurface imaging applications.

Sensing lesions in tissues with light

The use of light for probing and imaging of biomedical media offers the promise for development of safe, noninvasive, and inexpensive clinical imaging modalities with diagnostic ability. Various properties of light together with the ways it interacts with biological tissues may provide multiple windows to peer inside body organs. Principles and methods for extraction of information about body functions and lesions that capitalize on temporal, spectral, polarization, and spatial characteristics of transmitted light are briefly outlined. As illustrations of the potential and efficacy of light-based techniques, time-sliced and spectroscopic images of normal and cancerous human breast tissues recorded with a femtosecond Ti:sapphire laser and a broadly tunable Cr:forsterite laser, respectively, are presented.