Machine Learning Methods as a Cost-Effective Alternative to Physics-Based Binding Free Energy Calculations.

The rank ordering of ligands remains one of the most attractive challenges in drug discovery. While physics-based in silico binding affinity methods dominate the field, they still have problems, which largely revolve around forcefield accuracy and sampling. Recent advances in machine learning have gained traction for protein-ligand binding affinity predictions in early drug discovery programs. In this article, we perform retrospective binding free energy evaluations for 172 compounds from our internal collection spread over four different protein targets and five congeneric ligand series. We compared multiple state-of-the-art free energy methods ranging from physics-based methods with different levels of complexity and conformational sampling to state-of-the-art machine-learning-based methods that were available to us. Overall, we found that physics-based methods behaved particularly well when the ligand perturbations were made in the solvation region, and they did not perform as well when accounting for large conformational changes in protein active sites. On the other end, machine-learning-based methods offer a good cost-effective alternative for binding free energy calculations, but the accuracy of their predictions is highly dependent on the experimental data available for training the model.

Discovery of small-molecule positive allosteric modulators of Parkin E3 ligase.

Pharmacological activation of the E3 ligase Parkin represents a rational therapeutic intervention for the treatment of Parkinson's disease. Here we identify several compounds that enhance the activity of wildtype Parkin in the presence of phospho-ubiquitin and act as positive allosteric modulators (PAMs). While these compounds activate Parkin in a series of biochemical assays, they do not act by thermally destabilizing Parkin and fail to enhance the Parkin translocation rate to mitochondria or to enact mitophagy in cell-based assays. We conclude that in the context of the cellular milieu the therapeutic window to pharmacologically activate Parkin is very narrow.

Understanding allosteric interactions in hMLKL protein that modulate necroptosis and its inhibition.

Mixed Lineage Kinase domain-Like (MLKL), a key player in necroptosis, is a multi-domain protein with an N-terminal 4 helical bundle (4HB) and a pseudokinase domain (PsK) connected by brace helices. Phosphorylation of PsK domain of MLKL is a key step towards oligomerization of 4HB domain that causes cell death. Necrosulfonamide (NSA) binds to the 4HB domain of MLKL to inhibit necroptosis. To understand the molecular details of MLKL function and it's inhibition, we have performed a molecular dynamic study on hMLKL protein in apo, phosphorylated and NSA-bound states for a total 3 µs simulation time. Our simulations show increased inter-domain flexibility, increased rigidification of the activation loop and increased alpha helical content in the brace helix region revealing a form of monomeric hMLKL necessary for oligomerization upon phosphorylation as compared to apo state. NSA binding disrupts this activated form and causes two main effects on hMLKL conformation: (1) locking of the relative orientation of 4HB and PsK domains by the formation of several new interactions and (2) prevention of key 4HB residues to participate in cross-linking for oligomer formation. This new understanding of the effect of hMLKL conformations on phosphorylation and NSA binding suggest new avenues for designing effective allosteric inhibitors of hMLKL.

Role of Percutaneous Nephrostomy in Bladder Carcinoma with Obstructive Uropathy: A Story Revisited.

OBJECTIVE: To evaluate the role of percutaneous nephrostomy (PCN) in patients of carcinoma bladder presenting with obstructive uropathy. MATERIAL AND METHODS: We evaluated medical records of 33 patients of bladder cancer with obstructive uropathy that presented to a tertiary care hospital in north India from January 2015 to December 2016. Outcome measures included technical success rates, change in blood urea and serum creatinine (measured on Day 1, 7, and 14); and complications of PCN according to Society of Interventional Radiology Guidelines for Percutaneous Nephrostomy. RESULTS: PCN was done in 30 patients. The mean age of patients was 51 years (range 42-67). 24 patients were male and 6 patients were female. The technical success rates for PCN placement were 93.33%. In 12 patients there was no improvement after PCN insertion. Improvement in clinical condition/kidney function occurred in 18 patients. Out of these 6 patients underwent radical cystectomy with ileal conduit formation and palliative radiotherapy/chemotherapy was given to 5 cases. In the remaining 7 patients, after an initial improvement that lasted for 2 weeks after PCN progressive renal dysfunction developed due to malignancy. Minor complications of PCN were seen in 16.6% of patients and major complications were seen in 10 % of cases. CONCLUSION: In selected patients with bladder carcinoma with obstructive uropathy, PCN insertion may improve kidney function tests to normal levels and enable them to receive tumor-specific curative/palliative treatment.

Generation of Pairwise Potentials Using Multidimensional Data Mining.

The rapid development of molecular structural databases provides the chemistry community access to an enormous array of experimental data that can be used to build and validate computational models. Using radial distribution functions collected from experimentally available X-ray and NMR structures, a number of so-called statistical potentials have been developed over the years using the structural data mining strategy. These potentials have been developed within the context of the two-particle Kirkwood equation by extending its original use for isotropic monatomic systems to anisotropic biomolecular systems. However, the accuracy and the unclear physical meaning of statistical potentials have long formed the central arguments against such methods. In this work, we present a new approach to generate molecular energy functions using structural data mining. Instead of employing the Kirkwood equation and introducing the "reference state" approximation, we model the multidimensional probability distributions of the molecular system using graphical models and generate the target pairwise Boltzmann probabilities using the Bayesian field theory. Different from the current statistical potentials that mimic the "knowledge-based" PMF based on the 2-particle Kirkwood equation, the graphical-model-based structure-derived potential developed in this study focuses on the generation of lower-dimensional Boltzmann distributions of atoms through reduction of dimensionality. We have named this new scoring function GARF, and in this work we focus on the mathematical derivation of our novel approach followed by validation studies on its ability to predict protein-ligand interactions.

Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.

Accurately predicting receptor-ligand binding free energies is one of the holy grails of computational chemistry with many applications in chemistry and biology. Many successes have been reported, but issues relating to sampling and force field accuracy remain significant issues affecting our ability to reliably calculate binding free energies. In order to explore these issues in more detail we have examined a series of small host-guest complexes from the SAMPL6 blind challenge, namely octa-acids (OAs)-guest complexes and Curcurbit[8]uril (CB8)-guest complexes. Specifically, potential of mean force studies using umbrella sampling combined with the weighted histogram method were carried out on both systems with both known and unknown binding affinities. We find that using standard force fields and straightforward simulation protocols we are able to obtain satisfactory results, but that simply scaling our results allows us to significantly improve our predictive ability for the unknown test sets: the overall RMSD of the binding free energy versus experiment is reduced from 5.59 to 2.36 kcal/mol; for the CB8 test system, the RMSD goes from 8.04 to 3.51 kcal/mol, while for the OAs test system, the RSMD goes from 2.89 to 0.95 kcal/mol. The scaling approach was inspired by studies on structurally related known benchmark sets: by simply scaling, the RMSD was reduced from 6.23 to 1.19 kcal/mol and from 2.96 to 0.62 kcal/mol for the CB8 benchmark system and the OA benchmark system, respectively. We find this scaling procedure to correct absolute binding affinities to be highly effective especially when working across a "congeneric" series with similar charge states. It is less successful when applied to mixed ligands with varied charges and chemical characteristics, but improvement is still realized in the present case. This approach suggests that there are large systematic errors in absolute binding free energy calculations that can be straightforwardly accounted for using a scaling procedure. Random errors are still an issue, but near chemical accuracy can be obtained using the present strategy in select cases.

The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation.

Obtaining a detailed description of how active site flap motion affects substrate or ligand binding will advance structure-based drug design (SBDD) efforts on systems including the kinases, HSP90, HIV protease, ureases, etc. Through this understanding, we will be able to design better inhibitors and better proteins that have desired functions. Herein we address this issue by generating the relevant configurational states of a protein flap on the molecular energy landscape using an approach we call MTFlex-b and then following this with a procedure to estimate the free energy associated with the motion of the flap region. To illustrate our overall workflow, we explored the free energy changes in the streptavidin/biotin system upon introducing conformational flexibility in loop3-4 in the biotin unbound ( apo) and bound ( holo) state. The free energy surfaces were created using the Movable Type free energy method, and for further validation, we compared them to potential of mean force (PMF) generated free energy surfaces using MD simulations employing the FF99SBILDN and FF14SB force fields. We also estimated the free energy thermodynamic cycle using an ensemble of closed-like and open-like end states for the ligand unbound and bound states and estimated the binding free energy to be approximately -16.2 kcal/mol (experimental -18.3 kcal/mol). The good agreement between MTFlex-b in combination with the MT method with experiment and MD simulations supports the effectiveness of our strategy in obtaining unique insights into the motions in proteins that can then be used in a range of biological and biomedical applications.

A rare case of giant cell tumour (GCT) of bone with lung metastases.

A case of 16-year-old girl with giant cell tumour of right fibula is presented to us with bilateral lung metastases. In view of widespread bilateral lung metastatic lesions, the patient was given multimodality treatment. Chemotherapy followed by radiotherapy to the local site as well as lung bath has been given and has shown good response.

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.

We review our performance in the SAMPL5 challenge for predicting host-guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6-10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1.26 and 1.53 kcal/mol for the non-methylated octa-acid, 2.83 and 3.06 kcal/mol for the methylated octa-acid, and 2.77 and 3.36 kcal/mol for Cucurbit[2]uril host. While our results are in reasonable agreement with experiment, we focused on particular cases in which our estimates gave incorrect results, particularly with regard to association between the octa-acids and an adamantane derivative. Working on the hypothesis that differential solvation effects play a role in effecting computed binding affinities for the parent octa-acid and the methylated octa-acid and that the ligands bind inside the pockets (rather than on the surface) we devised a new solvent accessible surface area term to better quantify solvation energy contributions in MT based studies. To further explore this issue a, molecular dynamics potential of mean force (PMF) study indicates that, as found by our docking calculations, the stable binding mode for this ligand is inside (rather than surface bound) the octa-acid cavity whether the entrance is methylated or not. The PMF studies also obtained the correct order for the methylation-induced change in binding affinities and associated the difference, to a large extent to differential solvation effects. Overall, the SAMPL5 challenge yielded in improvements our solvation modeling and also demonstrated the need for thorough validation of input data integrity prior to any computational analysis.

A Retrospective Evaluation of Clinical Profile of Second Primary Head and Neck Cancer.

INTRODUCTION: Incidence of Second Primary Malignancy (SPM) after successful treatment of primary is increasing and may cause the problem for optimal treatment. AIM: This study was conducted retrospectively to analyse incidence, disease free survival between malignancies, pattern of treatment and outcome. MATERIALS AND METHODS: Sixteen out of 22 patients of previously treated cases of head and neck cancer those develop SPM of head and neck region managed over a period of January 2012 to December 2015 in Department of Radiotherapy-II, Pt. BD Sharma PGIMS, Rohtak were analyzed retrospectively. Sixteen patients with unresectable disease were given reirradiation with external beam radiotherapy. RESULTS: Median age of presentation of first malignancy was 27 years (Ranged 26 -65 years), whereas median age was 60 years for second malignancy (range 45-71 years). All patients were smokers during first malignancy; 87.5% (14/16) had historyof smoking during second malignancy. Oropharynx (50%) was most common site of presentation of primary tumor whereas oral cavity was most common site of presentation in second primary tumor. CONCLUSION: Incidence of Second primary head and neck tumor after successful treatment for primary Head and neck cancer are increasing due to newer treatment strategies, longer survival and follow up. Reirradiation, surgery and or chemotherapy are treatment modalities. However second primary tumor of this region are associated with poor prognosis.

Incorporation of side chain flexibility into protein binding pockets using MTflex.

The plasticity of active sites plays a significant role in drug recognition and binding, but the accurate incorporation of 'receptor flexibility' remains a significant computational challenge. Many approaches have been put forward to address receptor flexibility in docking studies by generating relevant ensembles on the energy surface. Herein, we describe the Movable Type with flexibility (MTflex) method that generates ensembles on the more relevant free energy surface in a computationally tractable manner. This novel approach enumerates conformational states based on side chain flexibility and then estimates their relative free energies using the MT methodology. The resultant conformational states can then be used in subsequent docking and scoring exercises. In particular, we demonstrate that using the MTflex ensembles improves MT's ability to predict binding free energies over docking only to the crystal structure.

Exploring the Management of Radiation Proctitis in Current Clinical Practice.

INTRODUCTION: Radiation proctitis is radiation induced rectal mucositis, occurring as a consequence to radiation therapy of the pelvic organs for various pelvic region malignancies. The management of radiation proctitis is extremely challenging as no recommended guidelines are available and limited number of studies are there in the literature involving the various treatment options. AIM: The aim of the study is the in-depth review of published literature to see the role of various treatment modalities in the management of radiation proctitis. MATERIALS AND METHODS: An integrative review was undertaken within PubMed, MEDLINE, PMC, GOOGLE SEARCH databases and articles published upto February 2015 were reviewed and analysed. A total of 54 studies were included. RESULTS: Literature suggests that non surgical therapies are the first line of treatment and surgery is reserved for advanced or refractory cases. Endoscopic therapies form the mainstay of treatment in managing the patients of radiation proctitis. Argon plasma coagulation and laser therapies are preferred. Radiofrequency ablation, cryoablation and mesenchymal stem cell therapy are the upcoming modalities. Medical therapy can be tried alone or in conjunction to endoscopic therapies. In the resistant or refractory cases, surgery can be looked for in the form of diversion or resection with or without anastamosis. CONCLUSION: Though, a number of options are available, still a lot can be explored in this field to improve the morbidity in the patients and to confirm the superiority of one treatment over other.

Comparative study of tumor markers in patients with colorectal carcinoma before and after chemotherapy.

BACKGROUND: Colorectal carcinoma (CRC), the second leading cause of cancer-related deaths in US, has a rising time-trend in India. Tumour markers in CRC are extensively researched, and there's still debate on their diagnostic and prognostic values. METHODS: In this hospital-based longitudinal study in north India, 51 male diagnosed CRC cases (pre-chemotherapy) were contrasted against 50 age and sex matched controls. Nine biomarkers: carcinoembryonic antigen (CEA), prolactin (PRL), alfa feto protein (AFP), total human chorionic gonadotropin (hCG), cancer antigen-125 (CA-125), serum testosterone, prostate specific antigen (PSA) and ferritin were measured by direct chemiluminescence technique. Further, follow-up was done on 47 cases after treatment with six cycles of 5-flurouracil (5-FU) and oxaliplatin. RESULTS: Mean serum CEA (case: 5.94±8.27 ng/mL, control: 2.5±0.79 ng/mL, P<0.05), PRL (case: 28.12±13.39 ng/mL, control: 14.24±13.13 ng/mL, P<0.0001), AFP (case: 10.9±6.65 ng/mL, control: 4.02±1.26 ng/mL, P<0.0001) levels were significantly raised in CRC cases compared to controls. On the contrary, mean testosterone level (P<0.05) was lower among the cases. After chemotherapy, the mean serum CEA (P<0.05), AFP (P<0.0001) and CA-125 (P<0.05) levels among the cases decreased significantly compared to their pretreatment levels. CONCLUSIONS: The present study strongly indicates the role of CEA, PRL, AFP, CA-125 and testosterone as important biomarkers in male CRC patients from north India. Further, AFP, CA-125 and CEA may be used to assess the effectiveness of chemotherapy in such patients.

Primary Non Hodgkin's Lymphoma of Left Adrenal Gland - A Rare Presentation.

Primary adrenal lymphoma is rare and constitutes for 3% of extranodal lymphoma cases. Approximately 70% of patients present with bilateral disease and have adrenal insufficiency. Prognosis of primary adrenal lymphoma (PAL) is poor, most of patient die within one year of diagnosis. Moreover, there are no standard treatment protocols on such cases. Patients are generally treated with regimens similar to other nonhodgkin lymphoma which includes surgery, combination chemotherapy and or radiotherapy. We are presenting a successfully treated case of primary diffuse large B cell non Hodgkin lymphoma of adrenal gland in a 57-year-old patient. The patient had unilateral adrenal involvement (left adrenal gland), without adrenal insufficiency and normal Serum lactate dehyrogenase level. The patient was treated with left adrenalectomy followed by combination chemotherapy. Two years after diagnosis and treatment the patient is disease free on clinical and imaging studies.

Current management approach to hidradenocarcinoma: a comprehensive review of the literature.

Hidradenocarcinoma is a rare malignant adnexal tumour which arises from the intradermal duct of eccrine sweat glands. The head and neck are the most common sites of hidradenocarcinoma, but rarely it can occur on the extremities. As it is an aggressive tumour, regional lymph nodes and distant viscera are the most common sites of metastasis. Diagnosis is confirmed by histopathology and immunohistochemistry. Hidradenocarcinoma should be differentiated from benign and malignant adnexal tumours. Being an aggressive and rare tumour, no uniform treatment guidelines have been documented so far for metastatic hidradenocarcinoma. Wide local excision is the mainstay of the treatment, but because of high local recurrence, radiotherapy in a dose of 50Gy-70Gy and/or 5-fluorouracil and capecitabine-based combination chemotherapy may be given to further improve local control. Other treatment strategies are targeted therapies like trastuzumab, EGFR inhibitors, PI3K/Akt/mTOR pathway inhibitors, hormonal agents like antiandrogens, electrochemotherapy, or clinical trials.

Microscopic hydration properties of the aß1-42 Peptide monomer and the globular protein ubiquitin: a comparative molecular dynamics study.

Atomistic molecular dynamics simulations of eight selected conformations of a disordered protein, amyloid beta (1-42) (Aß), and a globular protein, ubiquitin (UBQ), have been carried out in aqueous media at 310 K. Detailed analyses were carried out to compare the microscopic properties of water molecules present in the hydration layers of these systems. It is noticed that irrespective of the conformational heterogeneity among the Aß monomers, water molecules hydrating their surfaces exhibit relatively faster dynamics as compared to water molecules hydrating UBQ. Importantly, the conformational heterogeneity of the Aß monomers has been found to affect the translational and rotational motions of hydration water molecules in a nonuniform manner. Detailed investigation of the timescale of hydrogen bond relaxations at the surface and their energetics revealed the possibility of heterogeneous confinement around different Aß conformations. The distribution of water density fluctuation around Aß conformations are broader compared to UBQ because of its predominant hydrophobic nature. Significant heterogeneity in the density fluctuation among the Aß monomers suggests that the structural propensities could affect the peptide's effective surface hydrophobicity.