This document discusses the challenges of novel antibacterial discovery and potential strategies to address it. It notes that no new classes of antibiotics have been registered since 1984, despite efforts focused on single enzyme targets which often lead to resistance. Successful strategies may include pursuing multi-target agents less prone to resistance, understanding physicochemical properties required for entry into gram-negative bacteria, and taking a more empirical screening-based approach informed by these insights. Combination therapies may also help prevent resistance from single mutations. Overall, antibacterial discovery is a multi-faceted problem requiring consideration of targets, resistance potential, and mechanisms of bacterial entry and efflux.
This is a lecture by Dr. Jerry McLaughlin about his research into extracts of pawpaw plants, annonaceous acetogenins, in vitro, in vivo, mechanism of action, and toxicity in mice.
This is a lecture by Dr. Jerry McLaughlin about his research into extracts of pawpaw plants, annonaceous acetogenins, in vitro, in vivo, mechanism of action, and toxicity in mice.
Dana Vanderwall, Associate Director of Cheminformatics at Bristol-Myers Squibb, presented at Drexel University for Jean-Claude Bradley's Chemical Information Retrieval class on December 2, 2010. This first part covers "Cheminformatics & The evolving relationship between data in the public domain & pharma" and includes a general discussion of modern drug discovery and the details of a malaria dataset recently released from the pharmaceutical industry to the public.
An attempt was made to study the Cytogenetical effects of gamma rays and ethyl methane sulphonate on meiotic chromosomal abnormalities in two cultivars viz., PKV-1 and JS-335. The most frequently observed aberrations in meiosis were univalents, trivalent, multivalents chromosomal fragments, desynapsis of chromosome, laggards, and clumping of chromosomes etc. The physical mutagens were more effective than chemical mutagens. The effect of gamma-rays and ethyl methane sulphonate shows chlorophyll mutations such as Chlorina, Xantha, Albina, and Alboviridis in an M2 generation in both the cultivars. Cultivar JS-335 shows more pronounced effect than cultivar PKV-1. Gamma-rays recorded maximum macro mutations as compared to chemical mutagens (EMS). The frequency and spectrum of morphological mutation indicated that variety JS-335 was more sensitive than PKV-1. Different response of the two varieties to various mutagens was noticed. Key-words- Gamma radiation, EMS, Chromosomal aberrations, Mutagens, Chlorophyll mutation
Historically, genetic toxicology has been comprised of bacterial and cell based in vitro assays such as the Ames assay (a bacterial mutagenicity assay), Micronucleus and Chromosomal Aberration assays (mammalian cytogenetic assays), and Mouse Lymphoma Assay (in vitro mammalian cell gene mutation assay). These were routinely used for safety evaluation and are still part of the standard core battery. The emergence of new technologies has facilitated the development of in vitro methods for safe and effective drug and chemical testing.
This BioReliance® toxicology services webinar will explore alternative models, including 3D skin models that comply with the EC Scientific Committee on Consumer Safety (SCCS) recommendations. It will also discuss how the 3Rs (Replace, Reduce, Refine) Principle advocates the exploration of such alternative methods while achieving required goals.
In this webinar, you will learn:
• About in vitro alternatives to animal toxicity testing in pharma, chemical, tobacco, and personal care products.
• How the 3Rs (Replace, Reduce, Refine) Principle advocates exploring alternative methods without compromising the required goals.
• Alternatives to comply with the 7th Amendment to the EC Cosmetics Directive.
A study of antibiotic resistance of Extended-Spectrum Beta-Lactamases produci...Premier Publishers
Background: Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae are common in hospitals. This study aims to describe the antibiotic resistance of these bacteria and their associated demographic and clinical factors. Methods: It was a prospective study of 73 isolates of Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae for a period of six months from July to December 2019 in the laboratory of Befelatanana. Results: This study showed 73 (6.3%) isolates of Extended-Spectrum Beta-Lactamases- producing Enterobacteriaceae, represented by 25 (34.2%) isolates of Klebsiella spp, 24 (32.9%) isolates of Escherichia coli, 22 (30.1%) isolates of Enterobacter spp and 2 (2.7%) isolates of Proteus spp. The antibiotic resistance of these bacteria varied from 0% to 100% for all of the antibiotics tested. Resistance to aminoglycosides ranged from 0% (amikacin) to 69.9% (gentamycin). Resistance to quinolones ranged from 43.8% (levofloxacin) to 76.7% (nalidixic acid). Similarly, 60 (82.2%) isolates were resistant to cotrimoxazole and 25 (34.2%) isolates to chloramphenicol. Patients under 20 years (57.1%) (p=0.03), men (52.2%)(p=0.11; NS), patients with respiratory samples (83.3%)(p=0.004), with pus (61.9%)(p=0.02) and hospitalized in surgery and intensive care units (68.4%)(p=0.0009) were the most affected by these enterobacteria. Conclusion: Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae are responsible for severe infections and the majorities are multi-resistant bacteria.
Keywords: Beta-lactamase, Enterobacteriaceae, antibiotic resistance, amikacin, imipenem.
Science and technology of manipulating and improving microbial strains, in order to enhance their metabolic capacities for biotechnological applications, are referred to as strain improvement.
CDD: Vault, CDD: Vision and CDD: Models for Drug Discovery CollaborationsSean Ekins
A talk given at SERMACS 7th Nov 2015 in Memphis, describes CDD Vault, CDD Vision and CDD Models. In addition it also describes how the software is used in large and smaller scale collaborations for drug discovery.
Dana Vanderwall, Associate Director of Cheminformatics at Bristol-Myers Squibb, presented at Drexel University for Jean-Claude Bradley's Chemical Information Retrieval class on December 2, 2010. This first part covers "Cheminformatics & The evolving relationship between data in the public domain & pharma" and includes a general discussion of modern drug discovery and the details of a malaria dataset recently released from the pharmaceutical industry to the public.
An attempt was made to study the Cytogenetical effects of gamma rays and ethyl methane sulphonate on meiotic chromosomal abnormalities in two cultivars viz., PKV-1 and JS-335. The most frequently observed aberrations in meiosis were univalents, trivalent, multivalents chromosomal fragments, desynapsis of chromosome, laggards, and clumping of chromosomes etc. The physical mutagens were more effective than chemical mutagens. The effect of gamma-rays and ethyl methane sulphonate shows chlorophyll mutations such as Chlorina, Xantha, Albina, and Alboviridis in an M2 generation in both the cultivars. Cultivar JS-335 shows more pronounced effect than cultivar PKV-1. Gamma-rays recorded maximum macro mutations as compared to chemical mutagens (EMS). The frequency and spectrum of morphological mutation indicated that variety JS-335 was more sensitive than PKV-1. Different response of the two varieties to various mutagens was noticed. Key-words- Gamma radiation, EMS, Chromosomal aberrations, Mutagens, Chlorophyll mutation
Historically, genetic toxicology has been comprised of bacterial and cell based in vitro assays such as the Ames assay (a bacterial mutagenicity assay), Micronucleus and Chromosomal Aberration assays (mammalian cytogenetic assays), and Mouse Lymphoma Assay (in vitro mammalian cell gene mutation assay). These were routinely used for safety evaluation and are still part of the standard core battery. The emergence of new technologies has facilitated the development of in vitro methods for safe and effective drug and chemical testing.
This BioReliance® toxicology services webinar will explore alternative models, including 3D skin models that comply with the EC Scientific Committee on Consumer Safety (SCCS) recommendations. It will also discuss how the 3Rs (Replace, Reduce, Refine) Principle advocates the exploration of such alternative methods while achieving required goals.
In this webinar, you will learn:
• About in vitro alternatives to animal toxicity testing in pharma, chemical, tobacco, and personal care products.
• How the 3Rs (Replace, Reduce, Refine) Principle advocates exploring alternative methods without compromising the required goals.
• Alternatives to comply with the 7th Amendment to the EC Cosmetics Directive.
A study of antibiotic resistance of Extended-Spectrum Beta-Lactamases produci...Premier Publishers
Background: Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae are common in hospitals. This study aims to describe the antibiotic resistance of these bacteria and their associated demographic and clinical factors. Methods: It was a prospective study of 73 isolates of Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae for a period of six months from July to December 2019 in the laboratory of Befelatanana. Results: This study showed 73 (6.3%) isolates of Extended-Spectrum Beta-Lactamases- producing Enterobacteriaceae, represented by 25 (34.2%) isolates of Klebsiella spp, 24 (32.9%) isolates of Escherichia coli, 22 (30.1%) isolates of Enterobacter spp and 2 (2.7%) isolates of Proteus spp. The antibiotic resistance of these bacteria varied from 0% to 100% for all of the antibiotics tested. Resistance to aminoglycosides ranged from 0% (amikacin) to 69.9% (gentamycin). Resistance to quinolones ranged from 43.8% (levofloxacin) to 76.7% (nalidixic acid). Similarly, 60 (82.2%) isolates were resistant to cotrimoxazole and 25 (34.2%) isolates to chloramphenicol. Patients under 20 years (57.1%) (p=0.03), men (52.2%)(p=0.11; NS), patients with respiratory samples (83.3%)(p=0.004), with pus (61.9%)(p=0.02) and hospitalized in surgery and intensive care units (68.4%)(p=0.0009) were the most affected by these enterobacteria. Conclusion: Extended-Spectrum Beta-Lactamases - producing Enterobacteriaceae are responsible for severe infections and the majorities are multi-resistant bacteria.
Keywords: Beta-lactamase, Enterobacteriaceae, antibiotic resistance, amikacin, imipenem.
Science and technology of manipulating and improving microbial strains, in order to enhance their metabolic capacities for biotechnological applications, are referred to as strain improvement.
CDD: Vault, CDD: Vision and CDD: Models for Drug Discovery CollaborationsSean Ekins
A talk given at SERMACS 7th Nov 2015 in Memphis, describes CDD Vault, CDD Vision and CDD Models. In addition it also describes how the software is used in large and smaller scale collaborations for drug discovery.
Answering the Call to Arms: Tools for assessing the anti-infective potential ...Cassandra Quave
This is a presentation delivered at the 16th Annual Conference on the Science of Botanicals and 5th Annual Interim American Society of Pharmacognosy Meeting from April 11-14, 2016 in Oxford, MS, USA.
Abstract:
Answering the Call to Arms: Tools for Assessing the Anti-infective Potential of Natural Products in a Time of Rising Antibiotic Resistance
Quave CL1,2
1 Center for the Study of Human Health, Emory University, 550 Asbury Circle, Candler Library 107, Atlanta, GA 30322 USA. 2 Department of Dermatology, Emory University School of Medicine, 615 Michael Street, Whitehead 105L, Atlanta, GA 30322 USA.
As antibiotic resistance continues to rise, the pool of viable anti-infective therapeutic options is becoming rapidly exhausted. New therapies are in high demand and natural products are a likely source of novel bioactive compounds to meet this need. In particular, botanical secondary metabolites represent a rich pool for antibiotic discovery efforts. Plants are often the primary ingredients used in traditional anti-infective therapies, and yet their activity and mechanisms of action are often poorly understood. Much of the antibacterial research on botanical extracts and essential oils has focused on growth inhibitory studies using outdated methods limited in their ability to obtain an accurate assessment of bioactivity. The emergence of new molecular and bioanalytical tools for drug discovery provides a unique opportunity for application to natural products research.
Using Staphylococcus aureus as a model, tools for anti-infective testing of plant extracts will be reviewed, specifically focusing on the merits and limitations of each method. Examples include standardized methods for examining activity for the inhibition of growth (e.g., MIC, MBC), virulence (e.g., quorum sensing and toxin quantification) and pathogenesis (e.g., biofilms and antibiotic synergy). Data from our recent discoveries of novel biofilm [1] and quorum sensing [2,3] inhibitors isolated from medicinal plants (Rubus ulmifolius, Castanea sativa and Schinus terebinthifolius) will be presented in the review of these tools.
Acknowledgements: This work was supported by a grant from the National Institutes of Health, National Center for Complementary and Integrative Health (R01 AT007052). The content is solely the responsibility of the authors and does not necessarily reflect the official views of NCCIH or NIH.
References: [1] Quave CL, Estévez-Carmona M, et al. (2012) PLoS ONE, 7(1): e28737. [2] Quave CL, Lyles JT, et al. (2015) PLoS ONE, 10(8): e0136486. [3] Quave CL, Horswill AR (2014) Frontiers in Microbiology, 5: 706.
Mike generously is sharing this slide set which he presented at the 250th meeting of the ACS 2015 so that others who think they can not afford to run drug discovery can consider this economical distributed, virtual model….and to see CDD Vault in action.
Incidence rate of multidrug-resistant organisms in a tertiary care hospital, ...Apollo Hospitals
Antimicrobial resistance to microorganisms is a growing public health concern globally, especially in developing countries. This study was conducted to study the incidence rate of multidrug-resistant organisms with their antibiotic sensitivity pattern.
Dr Gokul Bangalore: Over the years antibiotic resistant infections have emerged as a serious threat world over. The mortality is increasing phenomenally and a serious thought should be given to prevent or at least delay the rapid development of resistance. Alexander Fleming clearly said in his speech when he received the Nobel prize in 1950, for the discovery of Penicillin, that if these antibiotics fall into wrong hands and misused, there will be increasing development of antibiotic resistance in bacteria ultimately pushing the world into pre antibiotic era. How true. The world is facing this now. Antibiotics are a single class of drugs which are maximally misused,abused, indiscriminately used and over used. Antibiotic stewardship programs should have been in place at least 40 years back when a pattern of resistance started emerging. Now every individual who prescribe antibiotics should think globally act locally. However there are a number of reasons for the failure of antibiotic stewardship programs. That is a different issue and addressed seriously.Gokul Bangalore: Dr. B. N. Gokul. MBBS, MD (Bangalore), Cert. HIC & ID (Sweden).
Former: Professor of Microbiology, NIMHANS, Bangalore,
Isolation, Characterization, and Antibiotics Resistance Profile of Staphyloco...AdeyemiKayode2
Isolation, Characterization, and Antibiotics Resistance Profile of Staphylococci from Indoor Air of the Students’ Halls of Residence at the Obafemi Awolowo University, Ile Ife, Nigeria.
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri ...Scientific Review SR
Multi drug-resistant (MDR) isolates of Staphylococcus aureus are on rise and are becoming a
challenge for timely and appropriate treatment. The present study was carried out with an objective to isolate
Staphylococcus aureus from clinical samples and determine their sensitivity. Out of 110 samples collected, 44
were shown to contained S. aureus. The isolates were subjected to antibiotic sensitivity tests using 10 different
and commonly used antibiotics by modified Kirby- Bauer disc diffusion technique. Out of the total isolates (42)
tested, only 7.1% were susceptible to all the antibiotics. Multiple resistance was eminent in over 92% with
highest occurrence in 4.8% where the entire antibiotics were resisted. Multiple antibiotic resistance indixes
(MAR index) indicated that 0.6 index occurred most (23.8%) followed by 0.5 (19.0%). On the other hand, 0.1
and 0.8 indexes were the lowest with 0.0% and 1.0% occurrence respectively. Ciprofloxacin was resisted by
most of the organisms (64.3%) while amoxicillin (64.3%) and streptomycin (61.9%) were most efficacious. With
over 90% isolate having MAR index ≥ 0.2, the multiple drug resistance by the S. aureus is quite alarming and
might suggest inappropriate antibiotic usage by the sampled population. Therefore, the need to strategize the
nature of antibiotic treatment against S. aureus and massive campaign on indiscriminate antibiotic use is urgent.
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri M...Scientific Review
Multi drug-resistant (MDR) isolates of Staphylococcus aureus are on rise and are becoming a challenge for timely and appropriate treatment. The present study was carried out with an objective to isolate Staphylococcus aureus from clinical samples and determine their sensitivity. Out of 110 samples collected, 44 were shown to contained S. aureus. The isolates were subjected to antibiotic sensitivity tests using 10 different and commonly used antibiotics by modified Kirby- Bauer disc diffusion technique. Out of the total isolates (42) tested, only 7.1% were susceptible to all the antibiotics. Multiple resistance was eminent in over 92% with highest occurrence in 4.8% where the entire antibiotics were resisted. Multiple antibiotic resistance indixes (MAR index) indicated that 0.6 index occurred most (23.8%) followed by 0.5 (19.0%). On the other hand, 0.1 and 0.8 indexes were the lowest with 0.0% and 1.0% occurrence respectively. Ciprofloxacin was resisted by most of the organisms (64.3%) while amoxicillin (64.3%) and streptomycin (61.9%) were most efficacious. With over 90% isolate having MAR index ≥ 0.2, the multiple drug resistance by the S. aureus is quite alarming and might suggest inappropriate antibiotic usage by the sampled population. Therefore, the need to strategize the nature of antibiotic treatment against S. aureus and massive campaign on indiscriminate antibiotic use is urgent.
Antimicrobial Sensitivity Pattern of Pseudomonas fluorescens after Biofield T...Mahendra Kumar Trivedi
Objective of this study was to investigate the effect of biofield treatment on antimicrobial sensitivity patternof P. fluorescens. P. fluorescens cells were procured from MicroBioLogics in sealed packs bearing the AmericanType Culture Collection (ATCC 49838) number.
Alan Lesniewicz Memorial Lecture at UIC - July 2015Cassandra Quave
This is the keynote lecture given at the University of Illinois at Chicago Garden Walk event in the department of Pharmacognosy. The objectives of the talk were:
·Discuss the role of medical ethnobotany in drug discovery efforts
·Explore state-of-the-art research techniques that examine the activity of botanical natural products with next generation antibiotic discovery efforts focused on “alternative targets”, such as bacterial communication systems
·Provide examples of current research underway by her group both in the field (especially through fieldwork in the Mediterranean) and the lab (natural product research on multidrug resistant bacteria).
Antibiotic resistance occurs when bacteria change in response to the use of these medicines. A growing number of infections – such as pneumonia, tuberculosis, gonorrhoea, and salmonellosis – are becoming harder to treat as the antibiotics used to treat them become less effective. Antibiotic resistance leads to longer hospital stays,higher medical costs and increased mortality.
An Evaluation of Biofield Treatment on Susceptibility Pattern of Multidrug Re...Mahendra Kumar Trivedi
Stenotrophomonas maltophilia (S. maltophilia) is a Gram-negative bacillus, an opportunistic pathogen, particularly among nosocomial infections. Multi-drug resistant strains are associated with very high rate of morbidity and mortality in severely immunocompromised patients. Present study was designed to evaluate the effect of biofield treatment against multidrug resistant S. maltophilia. Clinical sample of S. maltophilia was collected and divided into two groups i.e. control and biofield treated which were analyzed after 10 days with respect to control. The following parameters viz. susceptibility pattern, minimum inhibitory concentration (MIC), biochemical studies and biotype number of both control and treated samples were measured by MicroScan Walk-Away® system. The results showed an overall change of 37.5% in susceptibility pattern and 39.4% in biochemical study while 33.3% changes in MIC values of tested antimicrobials after biofield treatment. Further, the treated group of S. maltophilia has also shown a significant change in biochemical reactions followed by its biotype number as compared to control group. Biochemical reactions of treated group showed negative reaction to acetamide and positive reactions to colistin, glucose, adonitol, melibiose, arabinose, nitrate, oxidation-fermentation, raffinose, rhaminose, sorbitol, sucrose, and Voges-Proskauer as compared with control. The biofield treatment showed an alteration in MIC values of amikacin, amoxicillin/K-clavulanate, chloramphenicol, gatifloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotetan, ticarcillin/K-clavulanate, trimethoprim/sulfamethoxazole. Altogether, data suggest that biofield treatment has significant effect to alter the sensitivity pattern of antimicrobials and biotype number against multidrug resistant strain of S. maltophilia.
Similar to Why Novel Antibacterial Discovery is so Hard (20)
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
1. Why novel antibacterial discovery is
so hard and what to do about it
SWON Industry Workshop
September 22, 2016
Lynn L. Silver
LL Silver Consulting, LLC
2. The “Innovation gap”in novel classes
Obscures the “Discovery void”
Fischbach and Walsh, 2009
Oxazolidinones
Glycopeptides
Macrolides
Aminoglycosides
Chloramphenicol, Tetracyclines
- lactams
Mutilins
Sulfa drugs
Innovation gap
No registered classes of antibiotics were discovered after 1984
Between 1962 and 2000, no major classes of antibiotics were introduced
Discovery void
Lipopeptides
1950 1960 1980 1990 2000 20101940 1970
Quinolones, Streptogramins
3. Antibacterials at FDA 2000-2015
Compound Usage Class Active versus
resistance
Discovery of
class
Fail at
FDA
Pass at
FDA
Linezolid Systemic IV/oral Oxazolidinones MRSA 1978 2000
Ertapenem Systemic IV/IM Carbapenem 1976 2001
Cefditoren Systemic oral Cephalosporin 1948 2001
Gemifloxacin Systemic oral Fluoroquinolone 1961 2003
Daptomycin Systemic oral Lipopeptide MRSA 1984 2003
Telithromycin Systemic oral Macrolide+ EryR S. pneumo 1952 2004
Tigecycline Systemic IV Tetracycline+ TetR 1948 2005
Faropenem Systemic oral Penem 1978 2006
Retapamulin Topical Pleuromutilin MRSA 1952 2007
Dalbavancin Systemic IV Glycopeptide 1953 2007 2014
Doripenem Systemic IV Carbapenem 1976 2007
Oritavancin Systemic IV Glycopeptide+ VRE 1953 2008 2014
Cethromycin Systemic oral Macrolide+ EryR S. pneumo 1952 2009
Iclaprim Systemic IV Trimethoprim+ TrmR 1961 2009
Besifloxacin Ophthalmic Fluoroquinolone 1961 2009
Telavancin Systemic IV Glycopeptide+ VRE 1953 2009
Ceftobiprole Systemic IV Cephalosporin+ MRSA 1948 2009
Ceftaroline Systemic IV Cephalosporin+ MRSA 1948 2010
Fidaxomicin Oral CDAD Lipiarmycin 1975
Tedizolid Systemic IV/Oral Oxazolidinone 1978 2014
Avy-Caz Systemic IV Cephalosporin+BLI CRE 1948+ 2015
Ceftolozane Systemic IV Cephalosporin+BLI 1948 2014
4. Consider…
• If Big Pharma (and biotechs) have been largely
unsuccessful in finding novel antibacterials to
develop…
• Will that be reversed by
– Increasing financial incentives?
– Revising regulatory policy?
• What has prevented novel discovery?
• The need to address scientific obstacles
5. Inhibit bacterial growth
Small molecule ‘Leads’Small molecule ‘Leads’
Small molecule ‘Hits’Small molecule ‘Hits’
since the mid-90s
Gene-to-Drug Approach
Novel antibacterial targets
High Throughput Screening
Candidates
Genomics
Preclinical testing
Clinical Trials
Drug
Inhibit the enzyme
Inhibit bacterial growth by
inhibiting the enzyme
Druglike properties
Low resistance potential
ez
abez ab
Candidates
6. Why has it been so hard?
• Opportunity cost
– Too much time chasing “targets”
– Not enough time addressing rate limiting steps
• Rate limiting steps
– Defining resistance potential of targets
– Chemistry
• Getting things into cells & avoiding efflux
• Better chemical libraries / return to natural products
10. Based on existing antibacterial drugs…
• Successful monotherapeutic antibacterials
– Not subject to single-step mutation to high level resistance
because they are multi-targeted
• Current drugs inhibiting single enzymes
– Generally used in combination
because they are subject to single mutation to significant resistance
THUS: "Multitargets" are preferable to single enzyme
targets for systemic monotherapy
BUT: The search for single enzyme inhibitors has been the
mainstay of novel discovery for at least 20 years …
Silver, L. L. and Bostian, K. A. (1993). Antimicrob. Agents. Chemother. 37:377-83.; Silver, L. L. (2007). Nat. Rev. Drug Discov. 6:41-55.
11. If single enzyme targets give rise to
resistance in the laboratory…
• Determine if the in vitro (laboratory) resistance is likely to
translate to resistance in the clinic
– Standardize the use of models for evolution of resistance under
therapeutic conditions
• Hollow fiber system in vitro
• Animal models with high inoculum
– Is “overnight” resistance likely to occur?
• Develop fixed combinations
– To prevent resistance as in TB, HIV, HCV, etc.
• Pursue multitargets
12. “Overnight” resistance
GSK’052 (AN3365)
• Oxaborole inhibitor of Leucyl tRNA Synthetase
• Excellent Gram-negative spectrum
• In vitro resistance frequencies of >10-8
• In Phase 2b cUTI study, resistance occurred in 4 of 14 patients
post treatment (3 after one day of treatment)
• Mutants were highly fit and MICs raised >1000 fold
• This should have been predictable
Hernandez, V.,et al.. 2013. Antimicrob. Agents Chemother. 57:1394-1403.
Twynholm, M., et al. 2013. Poster -1251 at 53rd ICAAC, Denver
O'Dwyer, K., A. Spivak, et al. (2014). Antimicrob. Agents Chemother. epub
13. Hollow fiber (in vitro) resistance study of GSK’052
• GSK’052 dosed vs E. coli at high (108/ml) inocula
• Resistant mutants take over the population in one day
VanScoy, B. D., et al. 2013. Poster A-016 at 53rd ICAAC, Denver.
14. Antibacterial Multitargeting
GlcNAc
MurNAc PP-C55
Gyrase Topo IV
Lipid II
ciprofloxacin
daptomycin
vancomycin
gentamicin
tetracycline
chloramphenicol
linezolid
erythromycin
Target the products of multiple genes – or the product of
their function – such that single mutations cannot lead to
high level resistance
• Two or more essential gene products with
similar active sites: DNA Gyrase & Topisomerase IV
• Products of identical genes : rRNA
• Essential structures produced by a pathway where
structural changes cannot be made by single
mutations: Membranes
• These and other known multiargets have been pursued
• But no new multitargeted agents have reached the clinic…
17. But the spectrum may mislead
• Since the major permeability difference between Gram- and Gram+
is the OM, some assume that finding ways of transiting the OM and
avoiding efflux will allow Gram- entry
• This is an error based on the fact that OM-permeable and effluxΔ
Gram-negatives are sensitive to many Gram-positive drugs.
18. G- barriers to G+ agents
S. Aureus
MIC
E. coli MIC (g/mL) Major barrier MW ClogD7.4 / ClogP
wt lpxC tolC lpxC
tolC
Rifampicin 0.0008 5 0.005 2.5 0.005 823 2.8/3.6
fold wt 1000 2 1000 OM
Novobiocin 0.05 200 50 0.8 0.4 612 1.4/3.3
fold wt 4 250 500 Efflux
Erythromycin 0.25 250 3.9 1.0 0.25 732 2.9/3.9
fold wt 64 250 1000 Efflux & OM
Kodali S, Galgoci A, Young K et al.
J. Biol. Chem. 280(2), 1669-1677 (2005)
These G+ agents already have properties that allow them to cross the
cytoplasmic membrane
However, If you start with random inhibitors and endow them with
qualities allowing OM-passage and efflux-avoidance they are unlikely
to enter the cytoplasm
The physicochemical characteristics for OM passage and efflux
avoidance appear orthogonal to those for CM passage
19. Gram negative barriers
• The Outer Membrane (OM) of gram negatives adds an orthogonal
barrier to that of the cytoplasmic membrane
Penetration of OM through porins prefers small (<600 MW) hydrophilic, charged compounds
But highly charged molecules can’t penetrate the CM (unless actively transported)
Molecules that do penetrate can be effluxed from the cytoplasm – or periplasm
You could study the selectivity of the barriers, transporters, porins, pumps individually
OR – you could ask what kind of molecules can enter the gram negative cytoplasm?
OM
CM
periplasm
20. A Gestalt approach to Gram-negative entry
• Turn from characterizing barriers individually
• To characterizing compounds that can enter
• Can we develop rules for entry by studying existing
compounds?
• In 2008, O’Shea and Moser published the first
analysis of physicochemical characteristics of
registered antibacterials making the distinction
between G- and G+ actives
21. Antibacterials Are Chemically Unlike other Drugs
Gram-negative
Gram-positive only
Other drugs +
MW
cLogD7.4
O'Shea, R. O. and H. E. Moser (2008). J. Med. Chem. 51: 2871-2878.
22. Binning Antibacterials
O'Shea, R. O. and H. E. Moser (2008]
Silver, L. L. (2011). Clin. Microbiol. Rev. 24(1): 71-109 based on data from O’Shea and Moser)
0.50.5
( )
24. -12
-10
-8
-6
-4
-2
0
2
4
6
8
0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400
Gram-negative
GN Transported & AG
Gram-positive only
MW
CLogD7.4
Do we need more bins?
Silver, L. L. (2016) A Gestalt approach to
Gram-negative entry. Bioorg. Med. Chem.
131 compounds
25. Can we bin by route of entry?
• Measure entry of (thousands of)compounds
into the cytoplasm (independent of activity)
• Determine routes of entry through OM, efflux
potential, CM.
• Determine a set of physico-chemical and/or
structural parameters (rules) for each bin
26. Routes to the cytoplasm
OM
CM
periplasm
LPS &O-Ag
• Diffusion
– Hydrophilic molecules: Cross OM rapidly via porins, may avoid efflux –poor CM passage
– Lipophilic molecules: Cross OM slowly, can be effluxed – good CM passage
• Active
– Hydrophilic molecules cross OM via porins, CM via transporters [ATP or PMF driven]
• Self-promoted uptake [SPU] through OM
– Cationic molecules, avoid efflux, CM passage via ψ or anionic lipid sequestration
– Watch for toxicity!
• Trojan horse
– Piggyback on active or facilitated transport; must avoid rapid resistance
• OM permeabilizers and EPIs as adjuncts
– Combine with CM-transiting molecules [properties of Gram+ drugs]
ψ
aminoglycosidesfosfomycin
chloramphenicolalbomycin
27. Antibacterial Discovery is a Multipronged
Problem
• Rational drug discovery focuses on structural biology of
targets
– But single targets are resistance-prone
– Can we use combinations? Multitargets?
• For Gram-negative antibacterials, must also study
physicochemistry of entry, LPS structure, efflux.
– Can we devise rules based on routes of entry?
• Multiple parameters must be optimized simultaneously for
successful drug design
• Produce “Gram-negative” chemical libraries
– Screen more empirically