This document discusses the challenges of linking different names, structures, bioactivity data, and mixtures associated with drugs. It provides examples related to the drug atorvastatin to illustrate issues like: multiple names it has accumulated over time from its discovery to approval and generic versions; differences in structures submitted to databases that split the data; lack of explicit links between a drug and its active metabolites or tested combinations. Resolving these issues and accurately linking all relevant information is challenging due to the complex ecosystem of data sources and historical errors and inconsistencies that have accumulated over decades.
Supercritical fluid (CO2) chromatography for quantitative determination of se...Ratnakaram Venkata Nadh
In the present study, two cancer therapeutic drugs (docetaxel and bortezomib) were separated from their
potential impurities on a chromatographic platform by utilizing CO2 gas (supercritical state) and quantified.
The chromatographic separations were achieved on two short columns BEH-2EP (100mm 3mm, 1.7 mm)
and CHIRALPAK AD-3 (100 mm 4.6 mm, 3 mm) for docetaxel and bortezomib, respectively. The present
work describes the role of organic modifiers in the separation of polar compounds by supercritical fluid
chromatography. The two new methods were fully validated in accordance with the current ICH
(International Council for Harmonization of technical requirements for pharmaceuticals for human use)
guidelines. The stability indicating power of the methods was demonstrated from the stress studies
conducted on the injection formulations of the two compounds. The methods are precise with % RSD of
0.4, linear with the correlation coefficient of r2 $ 0.999 and accurate in the range of 50–150% of the
target assay concentration. The two methods can be equally employed for the assay determination of
docetaxel and bortezomib APIs as well.
Synthesis, spectral characterization and bioactivity studies of some S-substi...Jing Zang
A new series of 5-(4-Chlorophenyl)-1,3,4-Oxadiazol-2-thiol derivatives was prepared from 4-chlorobenzoic acid (1) by converting it successively into corresponding ester (2), carbohydrazide (3) and 5-(4-Chlorophenyl)-1,3,4-Oxadiazol-2-thiol (4). Finally the target compounds, 6a-l, were synthesized by stirring 4 with different electrophiles, 5a-l, in DMF using NaH as weak base and activator. The proposed structures of newly synthesized compounds were confirmed by spectroscopic techniques such as 1H-NMR, 13C-NMR, HR-MS and EI-MS. All synthesized compounds were evaluated for their anti-bacterial, antifungal, cytotoxicity and enzyme inhibition activities. The compounds, 6e and 6g exhibited significant inhibition activity against acetyl cholinesterase enzyme (AChE) and 6j moderate activity against butyryl cholinesterase enzyme (BChE). The molecule, 4 exhibited good MIC (minimum inhibitory concentration) value against all the bacterial and fungal strains taken into account.
Synthesis, characterization and molecular docking of sulphacetamideAmeena Kadar
This is our 7th SEM Practice School work related to Chemistry.
This ppt contains various docking, characterization of the anti-bacterial drug Sulfacetamide, one of the Sulfonamides.
Supercritical fluid (CO2) chromatography for quantitative determination of se...Ratnakaram Venkata Nadh
In the present study, two cancer therapeutic drugs (docetaxel and bortezomib) were separated from their
potential impurities on a chromatographic platform by utilizing CO2 gas (supercritical state) and quantified.
The chromatographic separations were achieved on two short columns BEH-2EP (100mm 3mm, 1.7 mm)
and CHIRALPAK AD-3 (100 mm 4.6 mm, 3 mm) for docetaxel and bortezomib, respectively. The present
work describes the role of organic modifiers in the separation of polar compounds by supercritical fluid
chromatography. The two new methods were fully validated in accordance with the current ICH
(International Council for Harmonization of technical requirements for pharmaceuticals for human use)
guidelines. The stability indicating power of the methods was demonstrated from the stress studies
conducted on the injection formulations of the two compounds. The methods are precise with % RSD of
0.4, linear with the correlation coefficient of r2 $ 0.999 and accurate in the range of 50–150% of the
target assay concentration. The two methods can be equally employed for the assay determination of
docetaxel and bortezomib APIs as well.
Synthesis, spectral characterization and bioactivity studies of some S-substi...Jing Zang
A new series of 5-(4-Chlorophenyl)-1,3,4-Oxadiazol-2-thiol derivatives was prepared from 4-chlorobenzoic acid (1) by converting it successively into corresponding ester (2), carbohydrazide (3) and 5-(4-Chlorophenyl)-1,3,4-Oxadiazol-2-thiol (4). Finally the target compounds, 6a-l, were synthesized by stirring 4 with different electrophiles, 5a-l, in DMF using NaH as weak base and activator. The proposed structures of newly synthesized compounds were confirmed by spectroscopic techniques such as 1H-NMR, 13C-NMR, HR-MS and EI-MS. All synthesized compounds were evaluated for their anti-bacterial, antifungal, cytotoxicity and enzyme inhibition activities. The compounds, 6e and 6g exhibited significant inhibition activity against acetyl cholinesterase enzyme (AChE) and 6j moderate activity against butyryl cholinesterase enzyme (BChE). The molecule, 4 exhibited good MIC (minimum inhibitory concentration) value against all the bacterial and fungal strains taken into account.
Synthesis, characterization and molecular docking of sulphacetamideAmeena Kadar
This is our 7th SEM Practice School work related to Chemistry.
This ppt contains various docking, characterization of the anti-bacterial drug Sulfacetamide, one of the Sulfonamides.
Design, Synthesis, and Characterization of New 1,3,5-Trisubstituted-2-pyrazol...BRNSS Publication Hub
Objective: The objective of the paper was to design, synthesis, and characterization of new 1,3,5-trisubstituted-2-pyrazolines derivative and to evaluate for analgesic potential. Materials and Methods: The 1,3,5-tri-substituted-2-pyrazolines derivatives have been synthesized by the reaction of chalcone derivatives with 4-hydrazinylbenzene sulfonamide hydrochloride and phenyl hydrazine hydrochloride. Total 16 compounds have been synthesized and characterized by the IR, 1HNMR, and mass spectral analysis. Proposed compounds have been evaluated for analgesic activity. The synthesized compounds also evaluated for the analgesic activity by the following two methods, that is, hot plate test method and acetic acid induced writhing in mice. Pentazocine and acetyl acetic acid were used as standard drug for compare the efficacy. Results and Discussion: The analgesic activity of the 16 synthesized compound series A1-A8, and B1-B8 has been evaluated using hot plate test method and acetic acid induced writhing in mice. The results of the evaluation have been viewed by taking pentazocine and acetyl acetic acid as the standard drug. In hot plate test, series A1-A8, shown delay the paw withdrawal latency time for compound A2 (10.30 s), A4 (9.45 s), A7 (11.65 s), and A8 (11.26 s) after 90 min. In series, B1-B8 shown delay the paw withdrawal latency time for compound B2 (9.10 s) and B7 (10.42 s) after 90 min, inhibit the pain sensation, and inhibit pain produced by thermal means. Synthesized compounds of series A1-A8, compounds A2, A5, A6, A7, and A8 were shown 83.00, 76.01, 80.34, 86.99, and 88.15 were shown percent inhibition, significantly (p<0.05 and p<0.001, respectively) and reduced the number of wriths induced by 0.6% acetic acid at the dose of 10 mg/kg. Acetylsalicylic acid (10 mg/kg) appears to be better effective in reducing the number of wriths, it significantly (P < 0.001) reduced the number of wriths by 99.0%. The compounds B1, B3, and B4 have shown least active activity. These all finding suggest that these synthesized compounds have the potential as analgesic agent. Conclusion: The 1,3,5-pyrazoline derivatives has been successfully synthesized and evaluated for analgesic activity of mice model and results data indicate that compounds A2, A5, A6, A7, and A8 were shown 83.00, 76.01, 80.34, 86.99, and 88.15%, and compounds B2, B7, and B8 were shown 72.25, 74.27, and 74.56% inhibitions. The presence of SO2NH2 is essential for analgesic activity.
CorMedix Inc. (AMEX:CRMD) is a pharmaceutical company that seeks to in-license, develop and commercialize therapeutic products for the treatment of cardiac and kidney (cardiorenal) disease.
Herbal drugs / herbal medicines include
herbs, herbal materials, herbal preparations and
finished herbal products, that contain as active ingredients, part of plants, or other plant materials, or combinations.
Herbal medicines comprise of therapies employing plant based products.
It is an integral part of Ayurveda and some indigenous medical systems.
Herbal drugs are becoming more popular in the modern world for their application to cure variety of diseases with less toxic effects and better therapeutic effects
A suppository is another way to deliver a drug. It's a small, round, or cone-shaped object that you put in your body, often into your bottom. Once it's inside, it melts or dissolves and releases its medication.
Abstract
A simple and accurate UV method has been developed for the simultaneous estimation of Hamycin and Ketoconazole cream formulation using SHIMADZU UV-Visible 1700 spectrophotometer by simultaneous equation method, with Acetonitrile: 0.5% w/v Ammonium acetate (80:20v/v) as a solvent. The absorbance maxima were found to be 381.5 nm for Hamycin and 243.5 nm for Ketoconazole. The percentage purity of cream formulation was found to be 99.08% for Hamycin and 98.22% for Ketoconazole. This method was also validated by checking the accuracy, precision, LOQ, LOD and Ruggedness. The %RSD shows within specification limits. The linearity profile shows coefficient of variation 0.99 for both drugs.
Intranasal delivery of drug loaded thiolated co-polymeric microparticles for...Gaurav Patil
E-Presentation at Two days 15th Indo-US virtual International Conference
on “Global advances in Pharmaceutical and Allied Science”
In collaboration with
APP Gujarat State branch, AAP American International branch,
AAP Pharmedu Healthcare Manag Division
This presentation deals with the brief study of functionalized graphene oxide nanoparticles for the delivery of model anticancer drug. It represents benefits of targeted drug delivery over the conventional drug delivery,
It is one of the remingtons journal club seminar which is part of masters degree progam in pharmacy.
In Ayurveda, Withania is widely claimed to have potent aphrodisiac, sedative, rejuvenative and life prolonging properties. It is also used as a general energy-enhancing tonic known as Medharasayana, which means ‘that which promotes learning and a good memory’ and in geriatric problems .
Licensed Establishments In Human Tissue Sector March 2010Sylvana Brannon
A list by the Human Tissue Authority listing all the licensed and certified cord blood banks, whose stored samples are accepted for transplants in the UK.
Design, Synthesis, and Characterization of New 1,3,5-Trisubstituted-2-pyrazol...BRNSS Publication Hub
Objective: The objective of the paper was to design, synthesis, and characterization of new 1,3,5-trisubstituted-2-pyrazolines derivative and to evaluate for analgesic potential. Materials and Methods: The 1,3,5-tri-substituted-2-pyrazolines derivatives have been synthesized by the reaction of chalcone derivatives with 4-hydrazinylbenzene sulfonamide hydrochloride and phenyl hydrazine hydrochloride. Total 16 compounds have been synthesized and characterized by the IR, 1HNMR, and mass spectral analysis. Proposed compounds have been evaluated for analgesic activity. The synthesized compounds also evaluated for the analgesic activity by the following two methods, that is, hot plate test method and acetic acid induced writhing in mice. Pentazocine and acetyl acetic acid were used as standard drug for compare the efficacy. Results and Discussion: The analgesic activity of the 16 synthesized compound series A1-A8, and B1-B8 has been evaluated using hot plate test method and acetic acid induced writhing in mice. The results of the evaluation have been viewed by taking pentazocine and acetyl acetic acid as the standard drug. In hot plate test, series A1-A8, shown delay the paw withdrawal latency time for compound A2 (10.30 s), A4 (9.45 s), A7 (11.65 s), and A8 (11.26 s) after 90 min. In series, B1-B8 shown delay the paw withdrawal latency time for compound B2 (9.10 s) and B7 (10.42 s) after 90 min, inhibit the pain sensation, and inhibit pain produced by thermal means. Synthesized compounds of series A1-A8, compounds A2, A5, A6, A7, and A8 were shown 83.00, 76.01, 80.34, 86.99, and 88.15 were shown percent inhibition, significantly (p<0.05 and p<0.001, respectively) and reduced the number of wriths induced by 0.6% acetic acid at the dose of 10 mg/kg. Acetylsalicylic acid (10 mg/kg) appears to be better effective in reducing the number of wriths, it significantly (P < 0.001) reduced the number of wriths by 99.0%. The compounds B1, B3, and B4 have shown least active activity. These all finding suggest that these synthesized compounds have the potential as analgesic agent. Conclusion: The 1,3,5-pyrazoline derivatives has been successfully synthesized and evaluated for analgesic activity of mice model and results data indicate that compounds A2, A5, A6, A7, and A8 were shown 83.00, 76.01, 80.34, 86.99, and 88.15%, and compounds B2, B7, and B8 were shown 72.25, 74.27, and 74.56% inhibitions. The presence of SO2NH2 is essential for analgesic activity.
CorMedix Inc. (AMEX:CRMD) is a pharmaceutical company that seeks to in-license, develop and commercialize therapeutic products for the treatment of cardiac and kidney (cardiorenal) disease.
Herbal drugs / herbal medicines include
herbs, herbal materials, herbal preparations and
finished herbal products, that contain as active ingredients, part of plants, or other plant materials, or combinations.
Herbal medicines comprise of therapies employing plant based products.
It is an integral part of Ayurveda and some indigenous medical systems.
Herbal drugs are becoming more popular in the modern world for their application to cure variety of diseases with less toxic effects and better therapeutic effects
A suppository is another way to deliver a drug. It's a small, round, or cone-shaped object that you put in your body, often into your bottom. Once it's inside, it melts or dissolves and releases its medication.
Abstract
A simple and accurate UV method has been developed for the simultaneous estimation of Hamycin and Ketoconazole cream formulation using SHIMADZU UV-Visible 1700 spectrophotometer by simultaneous equation method, with Acetonitrile: 0.5% w/v Ammonium acetate (80:20v/v) as a solvent. The absorbance maxima were found to be 381.5 nm for Hamycin and 243.5 nm for Ketoconazole. The percentage purity of cream formulation was found to be 99.08% for Hamycin and 98.22% for Ketoconazole. This method was also validated by checking the accuracy, precision, LOQ, LOD and Ruggedness. The %RSD shows within specification limits. The linearity profile shows coefficient of variation 0.99 for both drugs.
Intranasal delivery of drug loaded thiolated co-polymeric microparticles for...Gaurav Patil
E-Presentation at Two days 15th Indo-US virtual International Conference
on “Global advances in Pharmaceutical and Allied Science”
In collaboration with
APP Gujarat State branch, AAP American International branch,
AAP Pharmedu Healthcare Manag Division
This presentation deals with the brief study of functionalized graphene oxide nanoparticles for the delivery of model anticancer drug. It represents benefits of targeted drug delivery over the conventional drug delivery,
It is one of the remingtons journal club seminar which is part of masters degree progam in pharmacy.
In Ayurveda, Withania is widely claimed to have potent aphrodisiac, sedative, rejuvenative and life prolonging properties. It is also used as a general energy-enhancing tonic known as Medharasayana, which means ‘that which promotes learning and a good memory’ and in geriatric problems .
Licensed Establishments In Human Tissue Sector March 2010Sylvana Brannon
A list by the Human Tissue Authority listing all the licensed and certified cord blood banks, whose stored samples are accepted for transplants in the UK.
Innovating in the life sciences and health-care sector? You can’t escape the regulators! Before you make a costly mistake, learn from the experts who have been through the process before.
Whether you’re working on a therapeutic, an in vitro diagnostic or a medical device, come find out how to identify and mitigate challenges along the path to regulatory approval.
Drug discovery is an inventive process of identifying a compound or new medication based on knowledge of biological target, therapeutically useful in treating and curing a disease.
The process of drug discovery involves the identification of candidates,synthesis, characterization,screening,assays for therapeutic efficacy.
Once a compound has shown its value in these tests, it will begin the process of drug development prior to clinical trials.
CDSCO Biologicals - Rules, Regulations, Guidelines and Standards for Regulato...Mohamed Fazil M
M. Pharmacy - Pharmaceutical Regulatory Affairs (MRA)
1st Semester - Regulations and Legislation for Biologics (MRA 104T)
Unit 2 - Rules, Regulations, Guidelines and Standards for Regulatory Filing of Biologicals
CDSCO Biologicals
CMC, post approval regulatory affairs, etcJayeshRajput7
this document covers points such as CMC, post approval regulatory affairs, regulation for combination products, and medical devices, common technical document (CTD) and electronic common technical document (eCTD) format, industry and FDA liasion, ICH guidelines of ICH Q,S,E,M, regulatory requirements of EU, MHRA, TGA and ROW countries.
ETORICOXIB AND PREGABALIN OF METHOD DEVLOPMENT IN RPHPLC BY UPEXA BAVADIYAUpexaBavadiya
Development and Validation for Simultaneous Estimation of Etoricoxib and Pregabalin in Bulk and Tablet Dosage Form by RP-HPLC 2K21 GTU MASTER IN PHARMACY BY UPEXA BAVADIYA
Presented to David Gloriam's Group, Copenhagen, Feb 2020
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The theme will be presented from the perspective of both past involvement in peptide curation in the Guide to Pharmacology (GtoPdb) and in current searching for bioactive peptides in the wider ecosystem that includes ChEMBL and PubChem. The core problem is that peptides hang in limbo land between bioinformatics (BLAST) and cheminformatics (Tanimoto) neither of which provide optimal searching. Curating peptides in GtoPdb presents many challenges, including mapping endogenous peptides to Swiss-Prot cleavage annotations. For synthetic peptides, equivocal specification of modifications and exact positions of radiolabels are also problematic However, target-mapped citation-supported quantitative binding parameters are curated where possible. For those peptides falling below the PubChem CID SMILES limit of approximately 70 residues, GtoPdb has been using Sugar and Splice from NextMove Software to convert into CIDs. Specific problems associated with finding bioactive peptides in databases will be outlined.
Vicissitudes of target validation for BACE1 and BACE2 Chris Southan
Introduction/Background & Aims
The beta-amyloid (APP) cleaving enzyme (BACE1) was implicated as a drug target for Alzheimer's Disease (AD) back in 1999. In 2011, the paralogue, BACE2, became a new proposed target for type II diabetes (T2DM) having been reported to be the TMEM27 secretase regulating pancreatic beta-cell function [1]. By 2019 the accumulated evidence, including a swathe of failed clinical trials for BACE1 inhibitors, has produced a de facto de-validation of both targets in both diseases. As a learning exercise, the series of events leading up to this is reviewed here.
Method/Summary of work
Basic information about these two targets and the lead compounds against them were sourced via the IUPHAR/BPS Guide to Pharmacology (GtoPdb) as Target ids: 2330 and 2331, for BACE1 and 2, respectively. This was consolidated by a literature and patent review as well as following them in other databases. The most recent information on clinical trials was sourced from press releases.
Results/Discussion
GtoPdb annotates 24 lead compounds against BACE1 and 12 against BACE2. The corresponding counts mapped to these targets in ChEMBL are 8741 and 1377 making BACE1 one of the most actively pursued enzyme targets ever. Notwithstanding the massive global effort during 2018 Merck’s verubecestat and J&J’s atabecestat BACE1 inhibitors not only failed their Phase III endpoints but even appeared to worsen cognition in prodromal patients. In 2019 Amgen/Novartis stopped Phase II/III trials of umibecestat that also showed more cognitive decline in the treatment group compared to controls. BACE2 presented an anomalous situation in several ways. By 2016 both Novartis and Amgen declared their inability to reproduce the TMEM27 secretase turnover reported in 2011. Notwithstanding, Novartis and other companies have published patents on BACE2-specific inhibitors over several years and paradoxically verubecestat is more potent against BACE2 rather than 1 but was never tested for glucose-lowering. Equally puzzling is that one academic group is still publishing BACE2 inhibitors for T2D even post de-validation. One thing both targets have in common is the complete absence of genetic support from genome-wide disease association studies but this warning sign went unheeded.
Conclusions
The massive waste of resources on the pursuit of BACE1 as an AD target over the last two decades is catastrophic. This tale of de-validation is compounded for this paralogous pair of enzymes by the fact that the original evidence for BACE2 as a T2D target was eventually refuted. The story of these targets highlights a range of crucial pharmacological pitfalls that must be avoided in the future.
Reference(s)
[1] Southan C, Hancock J.M. (2013) A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet. 4:293.
In silico 360 Analysis for Drug DevelopmentChris Southan
Introduction:
Consequent to a memorandum of understanding between the Karolinska Institutet and the International Union of Basic and Clinical Pharmacology (IUPHAR) in 2018 a report on academic drug development, including guidelines (ADEV) has been drafted [1]. As part of this exercise, we conceived a triage for comprehensive informatics profiling around the compound, target, disease axis. We have termed this “in slico 360” (INS360) the aim of which was to support ADEV teams since they may lack either internal expertise or external support to do this on their own. Indeed, some past SciLifeLab Drug Discovery and Development Platform projects had been halted because of overlooked competitive impingements or insufficient target validation evidence.
Methods
We assessed the current database landscape, mostly public but including commercial, for potential utility for INS360. We were guided primarily by content coverage, usability, and reputation. We also explored some open property prediction resources for assay interference and toxicological inferences.
Results:
As a first-stop-shop, we selected the IUPHAR/BPS Guide to PHARMACOLOGY with ~900 ligand-target relationships captured via expert curation of journal papers Moving up in scale we evaluated ChEMBL at 1.8 million compounds with 1.1 million assay descriptions and 7,000 targets. With yet another jump we could search the patent corpus with 18 million extracted compounds in SureChEMBL. We explored PubChem that integrates these three with over 500 other sources linked to 96 million compounds, BioAssay results and connectivity into the NCBI Entrez system. The final jump in scale for document-to-chemistry navigation was represented by SciFinder with 155 million structures. On the target side, 360-exploration has the need to encompass literature, structure, genetic variation, splicing, interactions, and disease pathways. From their UniProt links, both GtoPdb and ChEMBL provide these entry points. Navigating genetic association data in support of target validation was enabled by the OpenTargets portal and the GWAS Catalog. We also fount servers that could produce prediction scores from chemical structures for a range of features important for de-risking development.
Conclusion:
This work scoped out initial resource choices for the INS360. We propose that not only ADEV operations but essentially any pharmacology research team has much to gain from this approach and many potential pitfalls can consequently be avoided when approaching key checkpoints, such as preparing a publication. However, support may be needed for both institutions and teams to get the best out of these complex and feature-rich databases.
[1] Southan C, (2019) Towards Academic Drug Development Guidelines, ChemRxiv pre-print no. 8869574
Will the correct BACE ORFs please stand up?Chris Southan
BACE1 and BACE2 are protease targets for Alzheimer's and diabetes, respectively but their validation is now questioned
Phylogenetic analysis can added functional insights
This came up against two key problems
A surprising prevalence of incorrect protein sequences predicted from genomes
Many BACE1 and BACE2 orthologues had truncation and/or indel errors.
Key phylogenetic representative genomes are languishing in an unfinished state
Some options for amelioration of these problems will be described
An update on the evolution of these enzymes will be shown
Look for new and potentially useful human 5HT2A-directed small molecule chemistry surfaced since the last meeting., check for compounds against as 5HT2A primary target but also combined inhibitors, poll round the key databases, literature and patents, earching challenges arise from synonym soup, complex cross-reactivities (see PMID 29679900) in vitro data gaps and in vivo polypharmacology
Quality and noise in big chemistry databasesChris Southan
Presented at Aug 2019 ACS by Antony Williams. Abstract: The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem
Progress in drug discovery and chemical biology is hugely enabled by curated document-assay-result-compound-target relationships (D-A-R-C-P) in open databases from resources such as the Guide to Pharmacology and ChEMBL. These are synergistically integrated into PubChem which pre-computes chemical similarity and connectivity between over 95 million structures and 5.6 million BioAssay results. It also links chemistry to documents via various additional routes including MeSH and large scale submissions from publishers. However, these efforts are patchy and very few journals facilitate such connectivity. There thus remains a massive shortfall in public D-A-R-C-P capture from decades of papers and patents. This presentation will cover these aspects and discuss their partial amelioration by options such as author-driven depositions and open lab-book approaches as used by Open Source Malaria
Looking at chemistry - protein - papers connectivity in ELIXIRChris Southan
This is a poster for the UK ELXIR meetin in Birmingham UK, Nov 2018. It is the summary of a blog-post https://cdsouthan.blogspot.com/2018/08/an-initial-look-at-elixir-chemistry.html that asses chemistry <> protein <> papers connectivity (C-P-P) for five ELIXIR resources
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
Welcome to the first live UiPath Community Day Dubai! Join us for this unique occasion to meet our local and global UiPath Community and leaders. You will get a full view of the MEA region's automation landscape and the AI Powered automation technology capabilities of UiPath. Also, hosted by our local partners Marc Ellis, you will enjoy a half-day packed with industry insights and automation peers networking.
📕 Curious on our agenda? Wait no more!
10:00 Welcome note - UiPath Community in Dubai
Lovely Sinha, UiPath Community Chapter Leader, UiPath MVPx3, Hyper-automation Consultant, First Abu Dhabi Bank
10:20 A UiPath cross-region MEA overview
Ashraf El Zarka, VP and Managing Director MEA, UiPath
10:35: Customer Success Journey
Deepthi Deepak, Head of Intelligent Automation CoE, First Abu Dhabi Bank
11:15 The UiPath approach to GenAI with our three principles: improve accuracy, supercharge productivity, and automate more
Boris Krumrey, Global VP, Automation Innovation, UiPath
12:15 To discover how Marc Ellis leverages tech-driven solutions in recruitment and managed services.
Brendan Lingam, Director of Sales and Business Development, Marc Ellis
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
Join Maher Hanafi, VP of Engineering at Betterworks, in this new session where he'll share a practical framework to transform Gen AI prototypes into impactful products! He'll delve into the complexities of data collection and management, model selection and optimization, and ensuring security, scalability, and responsible use.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
zkStudyClub - Reef: Fast Succinct Non-Interactive Zero-Knowledge Regex ProofsAlex Pruden
This paper presents Reef, a system for generating publicly verifiable succinct non-interactive zero-knowledge proofs that a committed document matches or does not match a regular expression. We describe applications such as proving the strength of passwords, the provenance of email despite redactions, the validity of oblivious DNS queries, and the existence of mutations in DNA. Reef supports the Perl Compatible Regular Expression syntax, including wildcards, alternation, ranges, capture groups, Kleene star, negations, and lookarounds. Reef introduces a new type of automata, Skipping Alternating Finite Automata (SAFA), that skips irrelevant parts of a document when producing proofs without undermining soundness, and instantiates SAFA with a lookup argument. Our experimental evaluation confirms that Reef can generate proofs for documents with 32M characters; the proofs are small and cheap to verify (under a second).
Paper: https://eprint.iacr.org/2023/1886
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
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Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
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GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
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https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
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The Metaverse is popularized in science fiction, and now it is becoming closer to being a part of our daily lives through the use of social media and shopping companies. How can businesses survive in a world where Artificial Intelligence is becoming the present as well as the future of technology, and how does the Metaverse fit into business strategy when futurist ideas are developing into reality at accelerated rates? How do we do this when our data isn't up to scratch? How can we move towards success with our data so we are set up for the Metaverse when it arrives?
How can you help your company evolve, adapt, and succeed using Artificial Intelligence and the Metaverse to stay ahead of the competition? What are the potential issues, complications, and benefits that these technologies could bring to us and our organizations? In this session, Jen Stirrup will explain how to start thinking about these technologies as an organisation.
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Elizabeth Buie - Older adults: Are we really designing for our future selves?
Which Drug Did You Mean ?
1. Which Drug Did You Mean?
Resolving the linkage spaghetti between
semantic names, structures, bioactivity
and mixtures
Christopher Southan
ChrisDS Consulting, Göteborg,
Sweden,
Prepared for BioIT, Boston, April
2012, Track 14, Tuesday
See also
http://cdsouthan.blogspot.se/2012/
06/will-real-bosinhib-please-stand-
up-take.html
[1]
2. History of Drug Names
Approximate timelines
[cpd registration system structure and ID------------------------------------------------------------]
[patent IUPAC or image--------------------------------------------------------------------]
[internal code name(s) externally blinded-------]
[code name(s) > structure declared externally -----]
[journal papers -----------------------------------------------------------------------]
[International Non-proprietary name INN]
[INN indexed in MeSH-----------------]
[USAN, BAN, JAN --------------------]
[brand name(s)-------------------]
[combination brand ]
[2]
4. Causes of Drug Linkage Spaghetti (I)
• Tautomer/stereo mutiplexing and structure interconversion differences (e.g.
complex antibiotics)
• Popular structures > 100s of submitters > many vendors > more noise
• Opaque ecosystem of primary submitters, secondary linkers, declared circularity,
cryptic circularity, and submitters having independent portals with different rules
• Older drugs accumulate 100’s of synonyms and database x-refs, with erros
• Accumulated wet assay results are dependent on how long the drug has been in
which public screening collection
• Deprecated structures not always refreshed between databases globally
• Pro-drugs, metabolites or tested combinations rarely have explicit x-refs
[4]
5. Causes of Drug Linkage Spaghetti (II)
• Literature extractions flowing into drug databases (including MeSH) can have
– Author errors and paucity of standards in the primary report
– No quality filtration at the result level
– Curation errors and different annotation rules
– No discrimination of independent de-novo checking from annotation recycling
• Large-scale patent extraction feeds into databases bring in
– Forests of analogues with no data links
– High redundency for drugs and leads
– Structural differences between pipeline outputs
– Opportunistic permutations of salts and mixtures
– Opportunistic virtual deuteration of all best-selling drugs
• Drug discovery operations use many drugs as reference compounds in their
internal screening collections . This means
– Name > structure cross-mapping, internal, public and commercial
– Integration of internal and external data across the same drugs
[5]
6. Atorvastatin
• The scale of links provides a good cross section of problems
• Relationship cross-mappings and the PubChem tool-box
facilitate navigation through the links
• External submissons get a substance ID (SID) which are
merged to compound records (CID) vi chemistry rules (see
PubChem documentation)
• This drug has accumulated years of submissions from different
sources, BioAssay entries and pharmacology literature links
• The parent CID 60823 has
– 99 synonyms
– 6 stero forms
– 70 cannonicaly-related structures
– 449 substance records
[6]
11. Drug BioAssay Data: Splitting by
Submitted Structure Differences
Mainly uHTS and counterscreens
from Scripps & Burnham
AIDs 406848-53 in ChEMBL –
(antimalarial assay specified salt)
ChEMBL Antimalarial strain assays
(also specified salt), in vivo plus
three target links
Mainly qHTS from NCGC, no hits
[11]
12. Pharmacological Activity in vivo is ~70% Active
Metabolites i.e. not Atorvastatin
Hazardous Substances Data
Bank x-ref in the CID, but no
direct links to the metabolites
(yet). Only one in-vitro assay CID 9851106
result for 9808225
CID 60823
CID 9808225
[12]
13. Salt Confusion (I) Atorvastatin Calcium
FDA packege
CID 656846 Mw 1209 insert lable,
CAS 344423-98-9 hemicalcium
trihydrate
CID 60822 Mw 1155
CAS 134523-03-8
INN = atorvastatin
USAN/BAN = atorvastatin
CID 11227182 Mw 598 calcium
[13]
14. Salt Confusion (II): What gets to Patients
CID 656846
CID 53252956
CID 23665101
No INNs, USANs or clinical trials entries for these salts
[14]
15. Mixtures: Problematic all Round
• Atorvastatin parent (CID 60823) has 379 mixture SIDs and 147 mixture CIDs
permuatated from 122 component CIDs
• Of the 122 components 58 have a MeSH pharmacology tag, 92 have
BioAssays results, 70 are in DrugBank, 101 are in ChEMBL, and 47 are below
200 mw (and thus probably salts not drugs)
• Of the 147 mixture CIDs, only the 2 atorvastatin dimers have assay results or
pharmacology so none of the drug mixtures have direct data links
• None are in DrugBank CIDs and only atorvastin calcium is in ChEMBL
• 138 of the 147 have been extracted from patents by Derwent/Thomson and
are unlikely to get data links
• The small number of important drug combinations that do have data and/or
trial results are difficult to identify
• Tested drug mixtures rarely get public code names, some get trade names but
never INNs
• Chemistry rules may split mixtures and synonyms in databases
• PubMed "Drug Combinations"[MeSH Term] = 54,186 but no SID or CID links
• Mixture components can be designated with space, / , + or ”co”
[15]
16. The Famous Polypill: A Fuzzy term
CID 44602839 Thomson Pharma
18 clinicaltrials.gov entries, but
only partial component links
aspirin 81 mg, enalapril 2.5 mg, atorvastatin 20 mg and hydrochlorothiazide 12.5 mg
(polypill) PMID: 21647425: Australian New Zealand Clinical Trials Registry
ACTRN12607000099426
DrugBank and TTD negative
[16]
17. Caduet: an Approved Combination
Drugbank Wikipedia
http://clinicaltrials.gov/ct2/show/NCT01107743
[17]
19. A more Recent Combination
But, QA149 is negative in PubChem, DrugBank and TTD
[19]
20. Spaghetti is Resolvable but Errors are Tough:
Will the Real LX4211 Please Stand up ?
http://cenblog.org/the-haystack/2012/03/liveblogging-first-time-disclosures-from-acssandiego/
See also: http://cdsouthan.blogspot.se/2012/03/live-chemical-structure-blogging-but.html
[20]
21. Summary
• You can navigate the linkage spaghetti in name, synonym, structure
bioactivity and mixture space, but this needs perspicacity and
circumspection.
• The current drug information ecosystem with multiple stakeholders seems
destined to remain ”fuzzy”
• Beyond informatics challenges the consequences, particularly from frank
errors, could be more serious
• WHO INNs and naming stems play a key positive role – but ;
– No open athoritative database - only 7000 PDF entries (!)
– No transparent coordination between USAN, FDA, MeSH, national offices, or
clinical trials registries
– Susceptable to commercial flanking tactics
• Drug combinations have a bright pharmacological future but a difficult
informatics one
• The fuzz includes scientific challenges (e.g. complex strucutures,
dynamic tautomerism, active metabolites, formulation differences,
paucity of standardised and comparable activity data.
• Efforts are being made to improve the situation, including from the
databases represented in this Workshop session.
[21]
22. Questions Welcome
ChrisDS Consulting: http://www.cdsouthan.info/Consult/CDS_cons.htm
Mobile: +46(0)702-530710, Skype: cdsouthan
Email: cdsouthan@hotmail.com
Twitter: http://twitter.com/#!/cdsouthan
Blog: http://cdsouthan.blogspot.com/
LinkedIN: http://www.linkedin.com/in/cdsouthan
Website: http://www.cdsouthan.info/CDS_prof.htm
Publications: http://www.citeulike.org/user/cdsouthan/publications/order/year
Citations: http://scholar.google.com/citations?user=y1DsHJ8AAAAJ&hl=en
Presentations: http://www.slideshare.net/cdsouthan
FYI : A short piece on identifying the names and molecular details of
drugs in clinicaltrials.gov
http://www.samedanltd.com/magazine/13/issue/166/article/3152
[22]