Identification of potent inhibitors for Leishmania donovani homoserine kinase: an integrated in silico and kinetic study

Leishmaniasis is caused by ∼20 species of Leishmania that affects millions in endemic areas. Available therapies are not sufficient to effectively control the disease, cause severe side effects and eventually lead to drug resistance, making the discovery of novel therapeutic molecules an immediate need. Molecular target-based drug discovery, where the target is a defined molecular gene, protein or a mechanism, is a rationale driven approach for novel therapeutics. Humans obtain the essential amino acid such as threonine from dietary sources, while Leishmania synthesize it de-novo. Enzymes of the threonine biosynthesis pathway, including the rate limiting Homoserine kinase (HSK) which converts L-homoserine into ortho-phospho homoserine are thus attractive targets for rationale driven therapy. The absence of HSK in humans and its presence in Leishmania donovani enhances the opportunity to exploit HSK as a molecular target for anti-leishmanials therapeutic development. In this study, we utilize structure-based high throughput drug discovery (SBDD), followed by biochemical validation and identified two potential inhibitors (RH00038 and S02587) from Maybridge chemical library that targets L. donovani HSK. These two inhibitors effectively induced the mortality of Leishmania donovani in both amastigote and promastigote stages, with one of them being specific to parasite and twice as effective as the standard therapeutic molecule.

An in-silico insight into the predictive interaction of Apolipoprotein-E with Epstein-Barr virus proteins and their probable role in mediating Alzheimer's disease

Recent reports suggest that persistent Epstein-Barr virus (EBV) infection and its recurrent reactivation could instigate the formation of proteinaceous plaques in the brain: a hallmark of Alzheimer's disease (AD). Interestingly, a major genetic risk factor of AD, the apolipoprotein E (ApoE), could also influence the outcome of EBV infection in an individual. The ApoE is believed to influence the proteinaceous plaque clearance from the brain, and its defective functioning could result in the aggregate deposition. The persistent presence of EBV infection in a genetically predisposed individual could create a perfect recipe for severe neurodegenerative consequences. Therefore, in the present study, we investigated the possible interactions between ApoE and various EBV proteins using computational tools. Our results showed possibly stable de-novo interactions between the C-terminal domain of ApoE3 and EBV proteins: EBV nuclear antigen-1 (EBNA1) and BamHI Z fragment leftward open reading frame-1 (BZLF1). The EBNA1 protein of EBV plays a crucial role in establishing latency and replication of the virus. Whereas BZLF1 is involved in the lytic replication cycle. The proposed interaction of EBV proteins at the ligand-binding site of ApoE3 on CTD could interfere with- its capability to sequester amyloid fragments and, hence their clearance from the brain giving rise to AD pathology. This study provides a new outlook on EBV's underexplored role in AD development and paves the way for novel avenues of investigation which could further our understanding of AD pathogenesis.Communicated by Ramaswamy H. Sarma[Figure: see text].

Identification of novel inhibitors targeting TIRAP interactions with BTK and PKCδ in inflammation through an in silico approach

Advanced computational tools focusing on protein-protein interaction (PPI) based drug development is a powerful platform to accelerate the therapeutic development of small lead molecules and repurposed drugs. Toll/interleukin-1 receptor (TIR) domain-containing adapter protein (TIRAP) and its interactions with other proteins in macrophages signalling are crucial components of severe or persistent inflammation. TIRAP activation through Bruton's tyrosine kinase (BTK) and Protein Kinase C delta (PKCδ) is essential for downstream inflammatory signalling. We created homology-based structural models of BTK and PKCδ in MODELLER 9.24. TIRAP interactions with BTK and PKCδ in its non-phosphorylated and phosphorylated states were determined by multiple docking tools including HADDOCK 2.4, pyDockWEB and ClusPro 2.0. Food and Drug Administration (FDA)-approved drugs were virtually screened through Discovery Studio LibDock and Autodock Vina tools to target the common TIR domain residues of TIRAP, which interact with both BTK and PKC at the identified interfacial sites of the complexes. Four FDA-approved drugs were identified and found to have stable interactions over a range of 100 ns MD simulation timescales. These drugs block the interactions of both kinases with TIRAP in silico. Hence, these drugs have the potential to dampen downstream inflammatory signalling and inflammation-mediated disease.

Elective oocyte cryopreservation for age-related fertility decline

PURPOSE

Women who pursue fertility at an advanced age are increasingly common. Family planning and sexual education have traditionally focused on contraception and prevention of sexually transmitted diseases. A focus should now also be placed on fertility awareness and fertility preservation. This manuscript aims to give an update on the existing evidence around elective oocyte cryopreservation, also highlighting the need for fertility education and evidence-based, individualized counselling.

METHODS

A thorough electronic search was performed from the start of databases to March 2020 aiming to summarize the existing evidence around elective egg freezing, the logic behind its use, patient counselling and education, success rates and risks involved, regulation, cost-effectiveness, current status and future perspectives.

RESULTS

Clinician-led counselling regarding reproductive aging and fertility preservation is often overlooked. Elective oocyte cryopreservation is not a guarantee of live birth, and the answer regarding cost-effectiveness needs to be individualized. The existing studies on obstetric and perinatal outcomes following the use of egg freezing are, until now, reassuring. Constant monitoring of short-term and long-term outcomes, uniform regulation and evidence-based, individualized counselling is of paramount importance.

CONCLUSIONS

Elective oocyte cryopreservation is one of the most controversial aspects of the world of assisted reproduction, and a lot of questions remain unanswered. However, women today do have this option which was not available in the past. Elective oocyte cryopreservation for age-related fertility decline should be incorporated in women's reproductive options to ensure informed decisions and reproductive autonomy.

lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs

Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs and potent regulatory elements in the living cells. High throughput RNA sequencing analyses have generated a tremendous amount of transcript sequence data. A large proportion of these transcript sequences does not code for proteins and are known as non-coding RNAs. Among them, lncRNAs are a unique class of transcripts longer than 200 nucleotides with diverse biological functions and regulatory mechanisms. Recent emerging studies and next-generation sequencing technologies show a substantial amount of lncRNAs within the plant genome, which are yet to be identified. The computational identification of lncRNAs from these transcripts is a challenging task due to the involvement of a series of filtering steps. We have developed lncRNADetector, a bioinformatics pipeline for the identification of novel lncRNAs, especially from medicinal and aromatic plant (MAP) species. The lncRNADetector has been utilized to analyse and identify more than 88,459 lncRNAs from 21 species of MAPs. To provide a knowledge resource for the plant research community towards elucidating the diversity of biological roles of lncRNAs, the information generated about MAP lncRNAs (post-filtering steps) through lncRNADetector has been stored and organized in MAPslnc database (MAPslnc, https://lncrnapipe.cimap.res.in). The lncRNADetector web server and MAPslnc database have been developed in order to facilitate researchers for accurate identification of lncRNAs from the next-generation sequencing data of different organisms for downstream studies. To the best of our knowledge no such MAPslnc database is available till date.

Frequency and degree of inter-trait association of maxillary Non-Metric Dental Crown Traits in the permanent dentitions of two states of India

Non-metric Dental Crown Traits are a principal source of information in forensic dentistry. However, inadequate data on the prevalence of these traits prompted this study to determine the frequency, sexual dimorphism and degree of inter-trait association in two different populations of India. Dichotomized data on the existence of non-metric features were recorded among individuals from Odisha (n=506) and Kerala (n=536) between 15 to 30 years of age. Cusp of Carabelli is the most common trait to occur (48 %) followed by shovelling of incisors (15%) and Bushman canine (14%). Bushman canine (p=0.045) and Cusp of Carabelli (p = 0.041) were found to be significantly expressed in Odisha and Kerala populations respectively. A strong association between shovelling of central incisor and Bushman canine with a likelihood ratio of 14.041 (p=0.001) was observed. This study will help in characterizing the Indian dentition and post-mortem dental profiling.

Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation

Pyrazinamide (PZA), a crucial component of anti-TB therapy, is a prodrug. PZA interacts with PncA protein to be converted into its functional form i.e. pyrazinoic acid (POA). It has unique feature to kill dormant tubercle bacilli of acidic environment. Although significance of pH environment in PZA activation has been investigated in several of previous studies, insight into the significant atomistic variations in the interaction pattern of PZA with PncA, at different pH environments, are still required to be explored. On the other hand, continuously emerging PncA mutants, associated with PZA resistance, have also become a serious threat for global TB control program. Therefore, the current study was designed to understand the role of pH environment in the PZA activation and to explore the PZA resistance mechanism in various PncA mutants. The study included various in silico experiments like molecular docking, MD simulation, binding free energy estimation, PCA and FEL. In our study, we have found pH-3 and pH-5 environment as a highly significant environment for PZA activation. It was found that protonation or deprotonation of PZA activation site (PAS) residues, majorly K48, D56, K96 and E107, resulted in rearrangement of the PAS according to the pH conditions. It has also been observed that positioning of PZA binding near to Fe²⁺ and residues of catalytic triad (i.e. D8, K96 and C138) also play a very crucial role in the activation of PZA. The overall insight from the current study may help to develop new therapeutics against PncA mutated PZA resistance.Communicated by Ramaswamy H. Sarma.

Screening of Anti-mycobacterial Phytochemical Compounds for Potential Inhibitors against Mycobacterium Tuberculosis Isocitrate Lyase

Background and Introduction: Tuberculosis (TB) is a leading infectious disease caused by Mycobacterium tuberculosiswith high morbidity and mortality. Isocitrate lyase (MtbICL), a key enzyme of glyoxylate pathway has been shown to be involved in mycobacterial persistence, is attractive drug target against persistent tuberculosis.

METHODS

Virtual screening, molecular docking and MD simulation study has been integrated for screening of phytochemical based anti-mycobacterial compounds. Docking study of reported MtbICL inhibitors has shown an average binding affinity score -7.30 Kcal/mol. In virtual screening, compounds exhibiting lower binding energy than calculated average binding energy were selected as top hit compounds followed by calculation of drug likeness property. Relationship between experimental IC50 value and calculated binding gibbs free energy of reported inhibitors was also calculated through regression analysis to predict IC50 value of potential inhibitors.

RESULTS

Docking and MD simulation studies of top hit compounds have identified shinjudilactone (quassinoid), lecheronol A (pimarane) and caniojane (diterpene) as potential MtbICL inhibitors.

CONCLUSION

Phytochemical based anti-mycobacterial compound can further developed into effective drugs against persistence tuberculosis with lesser toxicity and side effects.

No high Tibetan Plateau until the Neogene

The Late Paleogene surface height and paleoenvironment for the core area of the Qinghai-Tibetan Plateau (QTP) remain critically unresolved. Here, we report the discovery of the youngest well-preserved fossil palm leaves from Tibet. They were recovered from the Late Paleogene (Chattian), ca. 25.5 ± 0.5 million years, paleolake sediments within the Lunpola Basin (32.033°N, 89.767°E), central QTP at a present elevation of 4655 m. The anatomy of palms renders them intrinsically susceptible to freezing, imposing upper bounds on their latitudinal and altitudinal distribution. Combined with model-determined paleoterrestrial lapse rates, this shows that a high plateau cannot have existed in the core of Tibet in the Paleogene. Instead, a deep paleovalley, whose floor was <2.3 km above mean sea level bounded by (>4 km) high mountain systems, formed a topographically highly varied landscape. This finding challenges prevailing views on tectonic processes, monsoon dynamics, and the evolution of Asian biodiversity.

Abstract P5-14-07: Accuracy of psychosocial assessments in an online surgical decision aid developed for early breast cancer patients with resource and educational constraints

Background: Women with early breast cancer routinely face a choice between breast conservation therapy and mastectomy, and assume agency through shared decision making. However, for women with lower socioeconomic power or education, barriers such as access to understandable information, involvement of family in decision making, and a decreased sense of autonomy inhibits this agency. To better empower this population, a simple to understand, online, self-administered, conjoint analysis based decision aid called “Navya Patient Preference Tool” (PPT) is developed to be used outside the physician encounter. PPT is unique in its incorporation of several psychological scales that assess potential confounders of participation in shared decision making.

Methodology: This is a pre-planned analysis of the reliability and validity of the psychological scales used in all three arms of an IRB approved randomized controlled trial to assess PPT. Women with operable node negative breast cancer eligible for BCT or MRM at one of Asia's largest academic tertiary cancer centers were eligible. PPT trial consists of an initial conjoint analysis questionnaire analyzing implicit preferences for breast conservation given to the intervention arms. The following psychological scales were given to all patients regardless of randomization: Autonomy Preference Index (API), Traditional-Egalitarian Gender Roles (TEGR), Caregiving Role, Brief Resiliency Scale (BRS), Appearances Scale, and Decisional Conflict Scale (DCS). Cronbach's alpha as a measure of internal reliability for all scales, and correlations of scores with known demographic trends as a measure of external validity are calculated.

Results: Of the 102 patients enrolled, 30 completed PPT in English, 39 in Hindi, and 33 in Marathi, (vernaculars). 69/102 were in middle and lower socioeconomic groups (Kuppuswamy Index). 53/102 had completed less than high school education. Internal reliability of all scales were high, with Cronbach's alpha above 0.7: API 0.74, TEGR 0.78, Caregiving 0.7, BRS 0.7, Appearance 0.84. DCS was highly reliable at 0.91, and is the primary outcome measure for the RCT. Correlations in the dataset met those expected in real world data, suggesting external validity. For e.g., education was inversely correlated with traditional gender roles on TEGR (R -0.4, p &lt;0.01), and positively correlated with resilience on BRS (R 0.228, p &lt;0.05). Individual scale items that are unrealistic were not chosen by any of the 102 respondents (e.g.,. My doctor should not participate in my medical decisions), substantiating nuanced reading. 85% of patients “Strongly Agreed” on a 1-5 Likert scale that “The survey questions were easy to understand” (mean score 1.18/5. SD 0.4).

Conclusions: Women with limited education and low socioeconomic status complete the online, self administered PPT outside of a physician encounter, with high internal reliability and external validity. Decision Aids such as Navya PPT, which account for psychosocial confounders of agency, have the potential to benefit women otherwise marginalized from shared decision making.

Citation Format: Joshi S, Ramarajan L, Ramarajan N, Srivastava G, Begum F, Deshpande O, Tondare A, Nair N, Parmar V, Gupta S, Badwe RA. Accuracy of psychosocial assessments in an online surgical decision aid developed for early breast cancer patients with resource and educational constraints [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 P5-14-07.

Molecular and computational approaches to understand resistance of New Delhi metallo β-lactamase variants (NDM-1, NDM-4, NDM-5, NDM-6, NDM-7)-producing strains against carbapenems

The discovery of NDM-1 and its variants has caused the emergence of antibiotic resistance in the community and hospital setting, causing major concern for health care across the globe. New Delhi Metallo-β-lactamase is known to hydrolyse almost all β-lactam antibiotics. Studies have shown the hydrolytic activates of NDM-1 and some of its variants, however a comparative study of these NDM variants has not been explored in detail. Hence, we proposed to check their catalytic activity by performing a comparative study between NDM-1 and its variants. The study was initiated to clone NDM variants (NDM-1, NDM-4, NDM-5, NDM-6 and NDM-7) followed by overexpression of the recombinant proteins to check their hydrolytic properties against β-lactam antibiotics. The minimum inhibitory concentration of carbapenems antibiotics for bla_NDM-5 clone was found four fold increased, whereas no change was observed in the clones having other variants. The hydrolytic activity of carbapenem with NDM-5 variant was found to be augmented as per the kinetics parameter where Km was decreased and kcat, kcat/Km values increased as compared to the NDM-1. Molecular docking studies were employed to identify the variations in the binding ability among all NDM variants with imipenem or meropenem. Simulation studies at 100 ns showed a good stability of NDM-5 with imipenem and meropenem as compared to NDM-1. CD spectroscopy data revealed significant changes in the secondary structure of NDM variants. We conclude that NDM-5 showed higher hydrolytic activity as compared to other variants. This study provides a comparative analysis of the severity of NDM producing strains.

An insight into medicinal chemistry of anticancer quinoxalines

Quinoxalines are benzopyrazines containing benzene and pyrazine rings fused together. In the recent past, quinoxalines have attracted Medicinal Chemists considerably for their syntheses and chemistry due to their distinct pharmacological activities. Diverse synthetic protocols have been developed via multicomponent reactions, single pot synthesis and combinatorial approach using efficient catalysts, reagents, and nano-composites etc. Further, the versatility of the quinoxaline core and its reasonable chemical simplicity devise it extremely promising source of bioactive compounds. Therefore, a wide variety of bioactive quinoxalines has been realised as antitumour, antifungal, anti-inflammatory, antimicrobial, and antiviral agents. Already, a few of them are clinical drugs while many more are under various phases of clinical trials. Present review focuses on chemistry and pharmacology (both efficacy and safety) of quinoxalines and also provides some insight in to their structure-activity relationship.

Abstract P4-10-02: Validation of a clinical informatics system for online multidisciplinary expert opinions: Mapping treatment recommendations to the NCCN resource-Stratified framework

Background: Most cancer patients in Low and Middle Income Countries (LMIC) cannot afford effective, expensive, evidence based therapies. Therefore, oncologists must tailor treatment plans to individual resource constraints. To support this, NCCN has created a Resource-Stratified Framework® (NCCN-RSF), which is an evidence-based four-tier prioritization scheme. Further, only a fraction of patients in LMIC have ready access to oncologists. In India, there are only ˜1600 oncologists for 1.8 million patients. To bridge this gap, Navya's clinical informatics based mobile ExpertApp combines learning from evidence, prior tumor board decisions, patient resource constraints, and quick review from TMC NCG oncologists to recommend tailored treatment plans to patients via an online expert opinion service. 11865 patients in 22 LMIC have reached out to receive an online expert opinion through Navya (ASCO 2017). This study maps Navya to NCCN-RSF as an evidence-based index for resource-sensitive treatment selection.

Methods: All breast cancer patients who received an online expert opinion from TMC NCG Navya between July 1st 2014 and April 30th 2017 were included. Navya systematically gathered information on patient resource constraints (such as affordability for Trastuzumab). Navya recommendations (breast and nodal surgery, radiation site and fractionation, drug and dose density etc.) were mapped to NCCN-RSF resource tiers (Basic, Core, Enhanced, Parent guideline). Reasons were categorized for Navya recommendations not present in NCCN-RSF.

Results: 616 patients (36.3% metastatic), mostly from India, received 1203 recommendations. At the specific treatment protocol level, 88.3% of Navya recommendations mapped with at least one NCCN-RSF resource tier (Table 1). 78.5% mapped to the Enhanced tier. Only 8.6% of recommendations mapped to Parent guidelines, and did not require tailoring for resource constraints. Fewer than 2% recommendations mapped to Core and none to Basic. 11.7% recommendations were not present in NCCN-RSF, for minor reasons such as substitution of a drug within the same class (35.8%) (e.g., Epirubicin for Adriamycin), dose dense protocols (14.3%) (e.g., 3 weekly Paclitaxel vs weekly Paclitaxel), and recommending Trastuzumab for less than a year for patients unable to afford year long therapy (14.3%), currently not included in NCCN-RSF.

Table 1- Mapping Navya to NCCN RSFNCCN RSF TiersHIGH LEVEL: Multimodality treatment and sequencing (1203)INTERMEDIATE: Within modality treatment categories (1188)GRANULAR: Specific treatment protocols (1140)E.g.Neoadjuvant vs Adjuvant ChemoAnthracycline vs TaxaneHypofractionation vs Standard XRTAt least one Tier98.8%±0.696%±1.188.3%±2Enhanced94.4%±1.391%±1.778.5%±2.7Core1.9%±5.61.2%±5.71.2%±5.8Parent NCCN2.4%±5.63.8%±5.68.6%±5.5

Conclusion: Navya's treatment recommendations are sensitive to resource constraints and map to peer reviewed and evidence based NCCN RSF, primarily at the Enhanced tier. Navya's clinical informatics based online service scales access to resource constrained treatment selection for large numbers of patients in LMIC without easy access to oncologists.

Citation Format: Badwe RA, Gupta S, Feldman N, Pramesh CS, Ramarajan N, Srivastava G, Nair N, Anderson BO. Validation of a clinical informatics system for online multidisciplinary expert opinions: Mapping treatment recommendations to the NCCN resource-Stratified framework [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-10-02.

Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β

BACE-1 and GSK-3β both are potential therapeutic drug targets for Alzheimer's disease. Recently, both these targets received attention for designing dual inhibitors. Till now only two scaffolds (triazinone and curcumin) derivatives have been reported as BACE-1 and GSK-3β dual inhibitors. In our previous work, we have reported first in class dual inhibitor for BACE-1 and GSK-3β. In this study, we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3β through docking, molecular dynamics, binding energy (MM-PBSA). These computational methods were performed to estimate the binding affinity of naphthofuran derivatives towards the BACE-1 and GSK-3β. In the docking results, two derivatives (NS7 and NS9) showed better binding affinity as compared to previously reported inhibitors. Hydrogen bond occupancy of NS7 and NS9 generated from MD trajectories showed good interaction with the flap residues Gln73, Thr72 of BACE-1 and Arg141, Thr138 residues of GSK-3β. MM-PBSA and energy decomposition per residue revealed different components of binding energy and relative importance of amino acid involved in binding. The results showed that the binding of inhibitors was majorly governed by the hydrophobic interactions and suggesting that hydrophobic interactions might be the key to design dual inhibitors for BACE1-1 and GSK-3β. Distance between important pair of amino acid residues indicated that BACE-1 and GSK-3β adopt closed conformation and become inactive after ligand binding. The results suggested that naphthofuran derivatives might act as dual inhibitor against BACE-1 and GSK-3β.

A physicochemical descriptor based method for effective and rapid screening of dual inhibitors against BACE-1 and GSK-3β as targets for Alzheimer's disease

Due to multifactorial nature of Alzheimer's disease one target-one ligand hypothesis often looks insufficient. BACE-1 and GSK-3β are well established therapeutic drug targets and interaction between BACE-1 and GSK-3β pathways has also been established. Thus, designing of dual inhibitor for these two targets seems rational and may provide effective therapeutic strategies against AD. Recent studies revealed that only two scaffolds i.e. triazinone and curcumin act as a dual inhibitor against BACE-1 and GSK-3β. Thus, this discovery set the path to screen new chemical entities from a vast chemical space (∼10⁶⁰ compounds) that inhibit both the targets. However, small part of the large chemical space will only show biological activity for specific targets. Virtual screening of large libraries is impractical and computational expensive especially in case of dual inhibitor design. In the case of dual or multi target inhibitor designing, we screened the database for each target that further increases time and resources. In this study we have done physicochemical descriptor based profiling to know the biological relevant chemical space for BACE-1 and GSK-3β inhibitors and proposed the suitable range of important physicochemical properties, occurrence of functional groups. We generated scaffolds tree of known inhibitors of BACE-1 and GSK-3β suggesting the common structure/fragment that can be used to design dual inhibitors. This approach can filter the potential dual inhibitor candidates of BACE-1 and GSK-3β from non inhibitors.

Evaluation of the nutrient profile of Trachyspermum ammi L. seed under the influence of nanoparticles during germination

Trachyspermum ammi L. commonly known as Ajwain is an annual herb belonging to the family Apiaceae. It is enormously grown in Egypt, Iran, Pakistan, Afghanistan, and India as well as European region. Seeds of Ajwain were highly administered by traditional healers and usually employed for different ailments. Nanomaterials are known to have plant growth promoting effects, which could find applications in agriculture. In this study, the nanoparticles (NPs) showed the potential to enhance the primary metabolites when administered during germination. Therefore, nanoparticles elicitation can be used to increase the productivity, nutritional values and metabolite contents in Trachyspermum ammi L. This study aimed to provide new insight of the potential growth promoting effects of the nanoparticles () on plant system. Different concentrations of two nanoparticles, that is, iron pyrite (FeS2) and molybdenum disulphide (MoS2) at three different concentrations of 25ug/ml, 50ug/ml and 75ug/ml were tested on the seeds of Trachyspermum ammi L. The data indicated that nanoparticles enhanced the seedling growth as greener leafs and increased lengths of epicotyl and hypocotyls were seen. These nanoparticles also showed the potential to increase the contents of primary metabolites during germination and the total soluble protein content in seed was increased in nanoparticles-treated seeds as compared to control. The total protein profiling by SDS-PAGE indicated significant differences in number and molecular weights of protein bands upon exposure to nanoparticles.

Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease

BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.

Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria

CTX-M-15 are the most prevalent types of β-lactamases that hydrolyze almost all antibiotics of β-lactam group lead to multiple-antibiotic resistance in bacteria. Three β-lactam inhibitors are available for use in combination with different antibiotics of cephalosporine group against the CTX-M-15-producing strains. Therefore, strategies to identify novel anti β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we screened three novel non-β-lactam inhibitors against CTX-M-15 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Hence, we proposed a study to understand the binding mode of CTX-M-15 with inhibitors using bioinformatics and experimental approach. We calculated the dissociation constants (K_d), association constant (K_a), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets. Molecular dynamic simulation carried out for 25 ns, revealed that these complexes were found stable throughout the simulation with relative RMSD in acceptable range. Moreover, microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as a lead molecule for future drug candidates against β-lactamases-producing bacteria.

Abstract P1-14-01: Building an experience engine to make cancer treatment decisions using machine learning

Introduction: Experts at tertiary care centers provide solutions to complex cases not addressed by high quality evidence. They intuitively retrieve patterns from years of experience to make treatment decisions. Short of personal consultations, there is no way to access this vast “experience database.” Experience Engine (XE) is a machine learning solution to structure experiential knowledge relevant for decision making, derive a similarity metric for patients who have received similar treatments, and predict treatment decisions that experts are likely to recommend.

Methods: 277 patient histories relating to 743 breast cancer tumor board decisions at two tertiary care centers were abstracted as the training set for machine learning. 161 distinct histories relating to 496 decisions for a separate expert opinion service at one of the centers was the holdout test set. Data was structured into 690 features based on a novel ontology designed specifically for breast cancer decision making.

To uncover nonlinear similarities, (for example, treatments for younger patients with multiple comorbidities and elderly patients may be similar), treatment decisions were grouped by timing and modality into 13 groups, such as primary surgery, 1st line palliative chemotherapy, etc.

Similarity metric was derived using machine learning on the training set. The target for prediction was the specific treatment decision i.e. TAC or another adjuvant regimen. The primary endpoint was percent accuracy of agreement between XE's predicted decision and experts' actual decision in the holdout test set. Multiple similarity distance metrics including Bhattacharya, Eskin, Goodall, etc., and multiclass classification algorithms such as Extreme Gradient Boosted Trees, Support Vector Machines, etc., were systematically evaluated to arrive at the algorithms that best fit each treatment group.

Results: The winning XE algorithms were 71% to 89% accurate for the various treatment groups, in predicting the actual treatment decisions recommended by the experts. The most frequent treatments recommended across all groups were standard evidence based therapies, as are often recommended by experts. For instance, when XE recommended standard adjuvant therapies for Her2- patients, it was 88% to 97% accurate. When XE recommended nonstandard therapies for the same treatment group, it was 72% to 90% accurate, related to larger number of nonstandard therapies within each treatment group and smaller samples of patients who underwent each type of nonstandard therapy. XE learned to weigh features relating to comorbidities and toxicities when recommending nonstandard therapies.

Conclusion: Machine learning on a structured database of past treatment decisions made by experts, can yield a predicted treatment decision that an expert is likely to recommend for a new patient. By including complex decisions that consider toxicities and morbidities, a rich source of knowledge can be created. Despite the limited dataset, XE learned features that experts strongly consider when making decisions. XE has the potential to analyze variations in decision making at expert practices, assess when to recommend nonstandard therapies, and serve as a training tool for new oncologists to make expert grade treatment decisions.

Citation Format: Ramarajan N, Gupta S, Perry P, Srivastava G, Kumbla A, Miller J, Feldman N, Nair N, Badwe RA. Building an experience engine to make cancer treatment decisions using machine learning [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-14-01.

Molecular dynamics simulation and free energy landscape methods in probing L215H, L217R and L225M βI-tubulin mutations causing paclitaxel resistance in cancer cells

Drug resistance poses a threatening challenge for mankind, as the development of resistance to already well-established drugs causes serious therapeutic problems. Resistance to paclitaxel (Ptxl), a complex diterpenoid working as microtubule stabilizer, is one such issue in cancer treatment. Microtubule stabilizer drugs, stabilises microtubules upon binding to β-tubulin subunit of tubulin heterodimer thus causing mitotic arrest leading to death of cancer cell. Leucine point mutations viz. L215H, L217R, and L225M were reported for Ptxl resistance in various cancers. In the current study, molecular mechanism of these resistance causing mutations was explored using molecular docking, molecular dynamics (MD) simulation, binding energy estimation (MMPBSA), free energy decomposition, principle component analysis (PCA) and free energy landscape (FEL) methods. A total of five systems including unbound βI-tubulin (Apo), docked wild+Ptxl, L215H+Ptxl, L217R+Ptxl and L225M+Ptxl were prepared, and 50 ns MD simulation was performed for each system. Binding energy estimation indicated that leucine mutation reduces the binding affinity of Ptxl in mutant types (MTs) as compared to wild type (WT). Further, in contrast to WT Ptxl interactions with the M-loop (PHE270-VAL286), S6-S7 loop and H9-H10 were significantly altered in MTs. Results showed that in MTs, Ptxl had weak interaction with M-loop residues, while having strong affinity with S6-S7 loop and H6-H7 loop. Moreover, PCA and FEL analysis revealed that M-loop flexible region (THR274-LEU284) was strongly bound with Ptxl in WT preventing its flexible movement and the causing factor for microtubule stabilization. In MTs due to poor interaction with Ptxl, M-loop flexible region retains its flexibility, therefore unable to stabilize microtubule. This study will give an insight into the importance of M-loop flexible region interaction with Ptxl for microtubule stabilization. In addition, it clearly provides the molecular basis of Ptxl resistance mechanism in leucine MTs. This work will help in developing novel microtubule stabilizers molecules active against MTs.

Identification of pathologically insignificant prostate cancer is not accurate in unscreened men

Background:

Identification of men harbouring insignificant prostate cancer (PC) is important in selecting patients for active surveillance. Tools have been developed in PSA-screened populations to identify such men based on clinical and biopsy parameters.

Methods:

Prospectively collected case series of 848 patients was treated with radical prostatectomy between July 2007 and October 2011 at an English tertiary care centre. Tumour volume was assessed by pathological examination. For each tool, receiver operator characteristics were calculated for predicting insignificant disease by three different criteria and the area under each curve compared. Comparison of accuracy in screened and unscreened populations was performed.

Results:

Of 848 patients, 415 had Gleason 3+3 disease on biopsy. Of these, 32.0% had extra-prostatic extension and 50.2% were upgraded. One had positive lymph nodes. Two hundred and six (24% of cohort) were D'Amico low risk. Of these, 143 had more than two biopsy cores involved. None of the tools evaluated has adequate discriminative power in predicting insignificant tumour burden. Accuracy is low in PSA-screened and -unscreened populations.

Conclusions:

In our unscreened population, tools designed to identify insignificant PC are inaccurate. Detection of a wider size range of prostate tumours in the unscreened may contribute to relative inaccuracy.

Abstract P2-10-07: Ep-ICD overexpression associates with poor prognosis in invasive ductal carcinoma

Background: Despite improvements in treatment strategies recurrence rates are still high among breast cancer patients. This may be attributed to heterogeneous nature of breast cancers representing varied morphologic and biological features, behavior, and response to therapy. Even among breast tumors of similar histologic type and grade, prognosis varies. Currently, breast cancer prognosis assessment methods have limited accuracy, are expensive, and in 20-30% of cases lead to over-treatment with adverse effects. None of the currently known prognostic factors has the ability to predict accurately which breast cancer patients are at high risk of recurrence. Thus, there is an increasing need for identification and validation of prognostic markers for assessment of risk for disease recurrence in breast cancer patients.

Epithelial cell adhesion molecule (EpCAM) is a glycosylated, 30- to 40-kDa type I membrane protein, expressed in several human epithelial tissues and overexpressed in cancers, as well as in progenitors, normal and cancer stem cells, and is implicated in epithelial mesenchymal transition (EMT). Regulated intra-membrane proteolysis (RIP) of EpCAM by tumor-necrosis-factor alpha converting enzyme (TACE) results in shedding of its extracellular domain (EpEx) and release of intracellular domain, Ep-ICD, into the cytoplasm. Ep-ICD can signal into the cell nucleus by engagement of components of the Wnt pathway proteins including four and one half LIM domains protein 2 (FHL2), β-catenin and Lef, leading to activation of its oncogenic activity.

Objective. Evaluate the prognostic significance of Ep-ICD overexpression in invasive ductal carcinoma (IDC).

Methodology: Formalin fixed paraffin embedded (FFPE) tissue sections obtained from IDCs (n = 180) and normal breast tissues (n = 45) were used for immunostaining for Ep-ICD using specific monoclonal antibody. A semi-quantitative visual scoring of the immunostaining results for Ep-ICD based on percentage of tumor cells stained and intensity of scoring was used to compare the expression in breast cancers and normal tissues. Statistical analysis was carried out to determine the association of Ep-ICD expression with clinical outcome.

Results: Among the 180 IDCs analyzed, nuclear Ep-ICD was observed in 75 tissues (41.7%) while cytoplasmic positivity was observed in 145 tissues (80.6%). In comparison, nuclear Ep-ICD localization was observed only in 11 normal tissues (23.9%) and cytoplasmic positivity was observed in 39 normal tissues (86.7%). The nuclear / cytoplasmic Ep-ICD expression has been correlated with at least 5 years follow-up data of 180 breast cancer patients after primary treatment. Kaplan Meier survival analysis showed significantly reduced 5 year disease free survival in IDC patients showing nuclear positivity (p &lt; 0.001) or cytoplasmic positivity (p = 0.048). In Cox multivariate regression analysis, nuclear Ep-ICD overexpression emerged as an independent indicator of poor prognosis in IDCs (p = 0.008, H.R. = 81.18).

Conclusion: Among invasive ductal carcinomas of the breast, nuclear Ep-ICD overexpression predicts reduced 5-year disease free survival.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-10-07.

Long-term outcome with lenalidomide and dexamethasone therapy for newly diagnosed multiple myeloma

The combination of lenalidomide and dexamethasone (Len-Dex) is a commonly used initial therapy for newly diagnosed multiple myeloma (MM). Although the initial response rates and toxicity are well known, long-term outcome is not well described. We studied 286 consecutive patients with newly diagnosed MM initially treated with Len-Dex. The median (range) age at diagnosis was 63 (28-92) years, 166 (58%) patients ≤ 65 years and 175 (61%) male. The median estimated duration on Len-Dex was 5.3 months with overall response (≥ partial response) of 72%, including 26% with very good partial response or better. The median overall survival (OS) from the diagnosis was not reached (NR) and the estimated 5-year survival was 71%. The median time to first disease progression, irrespective of transplant status, was 30.2 months. Overall, 143 (50%) patients underwent stem cell transplant. The median OS was NR for patients ≤ 70 years and 5.8 years for the older patients (P=0.01). The 5-year OS estimate for patients in International Staging System stage 1, 2 and 3 were 82, 65, and 44% respectively. There were 21 new second malignancies after MM diagnosis (6.6%). The median survival exceeding 7 years reflects the efficacy of novel agents. The risk of second malignancies doesn't appear to be excessive in this population.

Accommodation: its relation to refractive errors, amblyopia and biometric parameters

AIM

To study accommodation in relation to different refractive errors, amblyopia and to measure the anatomical changes in the accommodating eye

MATERIALS AND METHODS

We studied the amplitude of accommodation (AA) in 150 patients in the age group 11 ± 30 years which included emmetropes, myopes, hypermetropes and hypermetropic amblyopes using the Royal Air Force (RAF) rule. The anterior chamber depth (ACD), axial length (AxL) and lens thickness (LT) changes during accommodation were measured using an A-scan. Myopes and hypermetropes were further divided based on the amount of refractive error : less than 2D, 2 -4D and greater than 4D.

RESULTS

Corrected low myopes had the highest accommodation amplitude (p less than 0.05) followed by emmetropes. Corrected hypermetropes were found to have the lowest amplitude of accommodation (p less than 0.05). The amblyopic eye had a significantly low AA compared to the non-amblyopic eye (p less than 0.05). ACD decreased (p less than 0.05) and LT increased (p less than 0.05) during accommodation. The AxL increase was maximum in myopes (p less than 0.05) followed by hypermetropes but the change was not significant in hypermetropes (p greater than 0.05).

CONCLUSION

The amblyopic eye has low amplitudes of accommodation proving the benefit of near adds in amblyopic patients. Prolonged near work might induce myopia in susceptible eyes by increasing the axial length.

A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors

The critical 8p22 tumor suppressor deleted in liver cancer 1 (DLC1) is frequently inactivated by aberrant CpG methylation and/or genetic deletion and implicated in tumorigeneses of multiple tumor types. Here, we report the identification and characterization of its new isoform, DLC1 isoform 4 (DLC1-i4). This novel isoform encodes an 1125-aa (amino acid) protein with distinct N-terminus as compared with other known DLC1 isoforms. Similar to other isoforms, DLC1-i4 is expressed ubiquitously in normal tissues and immortalized normal epithelial cells, suggesting a role as a major DLC1 transcript. However, differential expression of the four DLC1 isoforms is found in tumor cell lines: Isoform 1 (longest) and 3 (short thus probably nonfunctional) share a promoter and are silenced in almost all cancer and immortalized cell lines, whereas isoform 2 and 4 utilize different promoters and are frequently downregulated. DLC1-i4 is significantly downregulated in multiple carcinoma cell lines, including 2/4 nasopharyngeal, 8/16 (50%) esophageal, 4/16 (25%) gastric, 6/9 (67%) breast, 3/4 colorectal, 4/4 cervical and 2/8(25%) lung carcinoma cell lines. The functional DLC1-i4 promoter is within a CpG island and is activated by wild-type p53. CpG methylation of the DLC1-i4 promoter is associated with its silencing in tumor cells and was detected in 38-100% of multiple primary tumors. Treatment with 5-aza-2'-deoxycytidine or genetic double knockout of DNMT1 and DNMT3B led to demethylation of the promoter and reactivation of its expression, indicating a predominantly epigenetic mechanism of silencing. Ectopic expression of DLC1-i4 in silenced tumor cells strongly inhibited their growth and colony formation. Thus, we identified a new isoform of DLC1 with tumor suppressive function. The differential expression of various DLC1 isoforms suggests interplay in modulating the complex activities of DLC1 during carcinogenesis.

Use of a MET-specific photoprobe to identify bladder tumors in an orthotopic xenograft model of bladder cancer

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Background: Met over-expression has been found in bladder cancer (CaB). Stage and grade increases in urothelial carcinoma have been found to correlate with increases in Met expression. To assess whether molecular optical imaging could enhance the detection of bladder tumors, we used a Met-specific soluble photoprobe in an orthotopic xenograft model of bladder transitional cell carcinoma (TCC).

Methods: An orthotopic xenograft murine model of CaB was developed with T24-Luciferase-positive bladder cancer cells. Presence of tumor was confirmed by luciferase optical imaging (Xenogen IVIS) of mice, 4 weeks after TCC cell implantation. Mice were euthanized and their bladders removed and bivalved. Bladders were incubated for 30 minutes with unbound fluorophore (Cy5**, Peak emission at 675 nM) and subsequently for another 30 minutes with Cy5** bound to a Met-specific peptide. Fluorescence imaging (Maestro) was performed before and after each incubation period. Following imaging, presence of tumor was confirmed histologically.

Results: Cy5**-Met- peptide bound in sufficient density to tumor tissue in bladders for visualization by optical imaging. The tumor to normal bladder imaging ratio ranged from 2:1 to 8:1. Bladder regions with high uptake of Cy5**-Met-peptide corresponded to tumor areas confirmed by histological analysis.

Conclusions: Cy5**-Met-peptide successfully targets Met in an orthotopic xenograft model of bladder cancer. Our results suggest that this agent maybe useful for the enhanced visualization of bladder cancer tumors during cystoscopy.

No significant financial relationships to disclose.

Effect of the orally available MET inhibitor PF-2341066 on tumor burden and metastasis in an orthotopic xenograft model of bladder cancer

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Background: Met over-expression has been found in bladder cancer (CaB). However, to date, the effects of Met inhibition in CaB have not been reported. We used a small, orally available, highly specific Met-inhibitor currently on phase 2 clinical trials, to assess its effects in an orthotopic xenograft model of bladder transitional cell carcinoma (TCC).

Methods: An orthotopic xenograft murine model of TCC of the bladder was developed with T24-Luciferase positive bladder cancer cells. NIH 3T3 cells producing human hepatocyte growth factor (hHGF) were implanted subcutaneously in mice to provide a source of hHGF. Animals were treated with the selective Met inhibitor (PF-2341066) intra-peritoneally after positive detection of bladder tumor primary and/or metatastatic disease. Fluorescence imaging (Xenogen IVIS) of mice was performed weekly. Mice were euthanized 4 weeks after the start of treatment and their tissues studied histologically.

Results: PF-2341066 was found to reduce tumor burden to below detectable levels in both primary and metastatic sites in all mice treated. No noticeable side effects were detected in treated mice secondary to drug administration.

Conclusions: This study is the first to test a small orally available Met-selective inhibitor in an orthotopic, HGF-driven model of human CaB. Our results demonstrate that Met-inhibition by PF-2341066 reduces TCC tumor burden supporting its potential use in patients with bladder cancer.

No significant financial relationships to disclose.

Absence of Epstein-Barr virus in oesophageal squamous cell carcinoma

Aim-To identify the possible role of Epstein-Barr virus (EBV), in Chinese patients, in the pathogenesis of oesophageal squamous cell carcinoma.Methods-Formalin fixed, paraffin wax embedded tissues from 74 cases of oesophageal squamous cell carcinoma (28 with well differentiated, 27 with moderately differentiated and 18 with poorly differentiated carcinomas) were analysed for EBV using in situ hybridisation for EBV encoded small RNAs.Results-EBV was detected in only a few lymphocytes adjacent to the tumour epithelia in 14 (19%) cases of oesophageal carcinoma. The adjacent, non-pathological oesophageal tissue was EBV negative.Conclusions-EBV does not play a major role in the aetiology of oesophageal squamous cell carcinoma.

Accumulation of p53 protein in inverted transitional cell papilloma of the urinary bladder

Aims-To study the possible accumulation of p53 protein in inverted papilloma of the urinary bladder.Methods-Formalin fixed, paraffin wax embedded sections from 14 cases of inverted papilloma of the urinary bladder were studied retrospectively. Accumulation of p53 was detected by immunohistochemistry using a mouse monoclonal antibody directed against p53. p53 protein reactivity was scored as follows: 0 = 10%; 1 = 10% to <30%; 2 = 30% to <50%; and 3 = >50% of cells p53 positive.Results-The 14 sections were scored as follows: 3 in four cases; 2 in four cases; 1 in one case; and 0 in five cases. Overall, nine (64%) of the 14 cases were positive for p53 protein.Conclusions-The accumulation of p53 protein in inverted papilloma of the urinary bladder suggests that p53 may have has an important role in the neoplastic process of this tumour. However, the benign nature of inverted papillomas suggests that p53 protein accumulation is not related to tumour invasiveness and metastasis. p53 reactivity cannot be used as a marker of malignancy for urothelial neoplasia. Further studies are required to determine the role of p53 protein in the oncogenesis of urothelial neoplasms.

Frequent epigenetic inactivation of Rb1 in addition to p15 and p16 in mantle cell and follicular lymphoma

Dysregulation of cell cycle control is an important mechanism in carcinogenesis. Gene promoter hypermethylation is an alternative mechanism of gene inactivation. We analyzed the methylation status of the tumor suppressor components of the INK4/Rb pathway in mantle cell lymphoma and follicular lymphoma by methylation-specific polymerase chain reaction for p15, p16, p18, and Rb1 in 23 mantle cell lymphoma and 30 follicular lymphoma cases and lymphoma cell lines. The methylation-specific polymerase chain reaction results showed that in mantle cell lymphoma, frequent p16 (82%) but infrequent p15 (8.7%) or Rb1 (17.4%) hypermethylation occurred, with p16 and Rb1 hypermethylation being mutually exclusive (P=.01). In follicular lymphoma, frequent hypermethylation of p15 (36.7%), p16 (56.7%), and Rb1 (43.3%) occurred, with p15 and Rb1 hypermethylation being mutually exclusive (P=.05). Concurrent methylation of p15 and p16 occurred in 26.7% of patients with follicular lymphoma and 8.7% of patients with mantle cell lymphoma. Compared with mantle cell lymphoma, there was more frequent p15 (P=.025) hypermethylation but comparable Rb1 (P=.07) and p16 (P=.07) hypermethylation in follicular lymphoma. In a patient with follicular lymphoma with sequential biopsies, Rb1 was unmethylated and expressed at diagnosis but became methylated and down-regulated at relapse. Moreover, methylation analysis of these 4 genes in an additional 8 patients with grade I follicular lymphoma showed that Rb, but not the other genes, was preferentially methylated in grade II (P=.03). In summary, most patients with mantle cell lymphoma and follicular lymphoma had epigenetic aberrations targeting the INK4/Rb pathway. There is more frequent p16 hypermethylation in mantle cell lymphoma and p15 or Rb1 hypermethylation in follicular lymphoma. The role of Rb methylation in disease or histologic transformation in follicular lymphoma warrants further study.