Scaffolds Library

To meet customers’ drug discovery needs better, InterBioScreen Ltd. offers you the opportunity to obtain compounds synthesized around the Scaffolds from InterBioScreen’s libraries.

• Select from >2 500 unique synthetic and natural-based scaffolds
• Specify MW limits of screening compounds
• Define any other inclusion/exclusion parameters
• Be supplied with up to 200 – 500 compounds per scaffold
• Choose to have compounds supplied exclusively or non-exclusively
• Define timeframe of the project

With a network of nearly 3,000 chemists in well-equipped labs across East Europe and Central Asia states, Interbioscreen has the resources, expertise and infrastructure to synthesize screening compounds from the scaffolds of your choice. Scaffold approach is not combinatorial chemistry. This is a custom synthesis project, which means that if you select any number of scaffolds from the database, the chemist will synthesize from 100- 500 derivatives of that structure. Syntheses can be very different, some involving to 12 steps. The most value of this project is in that the synthesis is performed in accordance with the customer’s guidelines /filters. Each company has its own objectives and thus specific requirements to the compounds they would wish to obtain. Since the selection of scaffolds is customer’s, this means that the customer is the first to receive custom-made compounds of their choice.

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Scaffolds Library Collections

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February 17, 2022August 10, 2023

Building Blocks

The Building Blocks (BB) collection currently contains
over 13200+ natural and synthetic in-stock-available building blocks.

The classification of the Building Blocks is indicated in the following fields.

PA Primary Amines
SA Secondary Amines
AL Alcohols
AK Aldehydes & Ketones
CA Carboxylic Acids
ES Esters
AN Anhydrides & Haloanhydrides
PH Phenols
AA Aminoacids & their derivatives
PE Peptides & their derivatives
CH Carbohydrates & their derivatives
NU Nucleotides & Nucleosides
ST Steroids & Terpenoids
HAE Haloid Alkyles & Epoxydes
SH Thiols
OCC Other Chemical Classes or Polyfunctional reagents
HY Hydrazines & Hydrazones
IC Isocyanates
ITC Isothiocyanates
SC Sulfochlorides

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Building Blocks Collections
(You can download the SDF file by scrolling to the bottom.)

Building Blocks Search: Enter a list of catalog numbers, InChI, InChIKey or SMILES

February 17, 2022August 10, 2023

Bioactive Compounds

The Bioactive Compound (BIO) collection includes known potent enzyme substrates, inhibitors and activators, receptor agonists and antagonists, bioregulators and other biologically active compounds for use in assay development and validation.

BIO database currently contains 789 compounds. In addition to the chemical and physical properties, each compound is accompanied by data on its biological use, mechanism of action, biological source (where applicable) and literature references.

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Bioactive Compounds Collections

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February 17, 2022February 17, 2022

Natural Compounds

The Natural Compound (NC) collection is one of the world’s largest and this fact has been acknowledged by the companies which pursue screening programs in Japan, Europe and the US.

IBS started to build up the NC collection in 1984, and to-date it has grown to include over 68000 compounds. Originally the main contributors of natural compounds & derivatives were research institutes of the former Soviet Union, e.g. institutes for plant chemistry, bioorganic chemistry, botanical institutes, institutes for biochemistry of microorganisms, phytopathology of plants etc. With time, we have expanded our sources of rare and unique natural compounds and over the past decade the collection has considerably grown due to the influx of natural products from Asia, Latin America, some European centers for natural products etc. In percentage terms, the collection can be said to comprise 30 – 35% of strictly natural compounds isolated from plants, microorganisms, marine species etc.; approximately 40% are derivatives of natural compounds, i.e. modified alkaloids, terpenoids, flavonoids etc, and the remaining 25-30% are mimetics (analogs) of the strictly natural compounds, e.g. azosteroids, azocoumarins, conjugated isoindole systems, oxaterpenoids etc.

Of the whole NC library, 60 – 65% are compounds of plant origin; 5-10% were isolated from microorganisms, about 5% from marine species and the rest from other natural sources. All compounds have purity at 92-98%. The structures and stereochemistry are confirmed by various physicochemical analytical methods, including NMR (Brucker 300 – 500 MHz), mass spectroscopy and in some cases X-ray analysis.

The most representative classes include various types of alkaloids (several thousand compounds), terpenoids (several thousand), flavonoids and coumarins (over 3 000 compounds), peptides, glycosides and nucleosides (over 1 000 compounds), phenol compounds (several hundred). The collection is also rich in rare and unusual compounds, such as various classes of phytoalexins, allelopathic agents, specific sex attractants, natural toxins, unusual sesquiterpenoids and other secondary metabolites. Apart from this, we also have a collection of functionalized natural compounds which can be used in Natural Combinatorial Chemistry as natural matrices. Compounds in this collection are available in the amounts from several grams up to several hundred grams. As a rule, we package natural compounds in vials or microplates as 2 mg – 5 mg – 10 mg – 20 mg – 50 mg samples.

Natural Compounds Collections

Natural Compounds Search: Enter a list of catalog numbers, InChI, InChIKey or SMILES

February 17, 2022February 17, 2022

Synthetic Compounds

The Synthetic Compound (SC) collection contains over 485000 immediately available compounds.

Part of the integrated IBS SC collection is composed of the best of the Syntest Ltd., NELBI Ltd., ChemEx Inc., ExiMed Ltd. collections. Interbioscreen has purchased these selected sub-collections which are now Interbioscreen’s property. The synthetic library of IBS is built around functionalized heterocyclic drug-like molecules. Most of these cannot be obtained combinatorially. From the very start, IBS has been generating its library by making a very strict selection of the most interesting classes of compounds which have potential of becoming new drugs or plant protection agents or preparations for use in veterinary. We were less interested in simple hydrazones, hydrazides, Schiff’s bases or readily decomposing compounds. The major criterion for the inclusion of a compound in the collection has been the novelty, abundance in pharmacophores, diversity and the “drug-like molecule” structure.

Synthetic Compound (SC) collection

Synthetic Compound (SC) Search: Enter a list of catalog numbers, InChI, InChIKey or SMILES

February 16, 2022February 17, 2022

Compounds

World leading provider of high quality chemical libraries for screening programs since 1998

SYNTHETIC COMPOUNDS

The Synthetic Compound (SC) collection contains over 485000 immediately available compounds.

NATURAL COMPOUNDS

The Natural Compound (NC) collection is one of the world’s largest and this fact has been acknowledged by the companies which pursue screening programs in India, Japan, Europe and the US.

BUILDING BLOCKS

The Building Blocks collection currently contains over 13000 natural and synthetic in-stock-available building blocks.

BIOACTIVE COMPOUNDS

Scaffolds Library

To meet customers’ drug discovery needs better, InterBioScreen Ltd. offers you the opportunity to obtain compounds synthesized around the Scaffolds from InterBioScreen’s libraries.

February 12, 2022February 12, 2022

A Better Way to Isolate DNA From Plant Tissues

CTAB PROTOCOL FOR ISOLATING DNA FROM PLANT TISSUES

THE CONVENTIONAL PLANT DNA EXTRACTION METHOD AND A STREAMLINED ALTERNATIVE

Modern genomics techniques have promised to revolutionize plant biology, generating data to accelerate crop improvement, optimize plant selection, and advance our basic understanding of plant biology.¹ Such techniques and applications rely on the extraction of high-quality DNA from a variety of distinct plant species and sample types.

To keep up with this rapidly advancing field, DNA extraction protocols must be robust, flexible, consistent, and fast. But plant tissues pose several challenges for even the most tried-and-true DNA extraction protocols. Plant cell walls are very difficult to break down and the cells contain many compounds that impede extraction and inhibit downstream molecular biology applications.

The CTAB Method: DNA Extraction from Plant Leaves and Seeds

To overcome the challenges presented by plant tissues, the cetyltrimethylammonium bromide (CTAB) method has become the “go-to” protocol for DNA extraction and purification from leaves and seeds. It was developed in the 1980s and has been used ever since, with various modifications for different plant species.^2-5

In the CTAB procedure, the first step is breaking down the tissue, and it involves freezing your plant sample using liquid nitrogen. Once the tissue has been frozen, it’s ground into a fine powder with a mortar and pestle or a blender. After grinding, the tissue is transferred to a tube and CTAB buffer is added. The CTAB buffer facilitates cell lysis and prevents secondary metabolites from interfering with DNA extraction and downstream procedures.

Following plant cell lysis, RNase A is added to digest RNA, and DNA is separated from other cellular components using phenol/chloroform extraction, which separates the sample into two distinct aqueous and organic phases after centrifugation. Nonpolar molecules migrate into the organic phase and leave behind DNA and other polar molecules in the aqueous phase. The extraction is repeated on the aqueous phase until it becomes completely clear, and all DNA is collected. The aqueous phase is collected, and the recovered DNA is precipitated out with isopropanol. The precipitate is pelleted by centrifugation and washed with 70% ethanol to remove salts introduced during extraction. Once the ethanol is decanted, the residual ethanol in the pellet is evaporated away and the dried pellet is resuspended in your buffer-of-choice for your downstream application, such as PCR or NGS.

Considerations Before Performing CTAB DNA Extraction

The CTAB method is biochemically simple, easy to learn, and relatively cheap to perform. However, in practice, the protocol has several drawbacks: it’s lengthy, tedious, and low throughput, with many steps that require careful handling, exposure to hazardous chemicals, and several other technical considerations.

Timing Your DNA Extractions

From grinding with a mortar and pestle to resuspending sticky DNA pellets, the full CTAB protocol can take approximately two hours to process a small number of samples. There are also more than 20 steps in the protocol and as the number of samples increases, the amount of time needed to complete DNA extraction increases substantially. Plan your day carefully and set aside the proper amount of time to complete the entire protocol.

Working With Hazardous Materials

Caution must be taken when working with liquid nitrogen for the first grinding step as it can rapidly freeze skin tissue and cause cold burns even with short exposure. In addition, working with phenol and chloroform is also a biosafety hazard: Phenol can cause chemical burns and chloroform is a potential carcinogen.^6,7 For many food testing labs, the use of these toxic chemicals is a major concern. Use of phenol/chloroform also generates organic waste which requires special storage containers and disposal procedures. Be sure you have the proper safety protocols in place before starting your DNA extractions.

Processing the Plant Tissue

Tissue grinding can vary between samples, leading to significant variation in extraction efficiencies and quality of DNA. To achieve more consistent tissue disruption across samples, you can also use a blender, though this step is still low throughput and time consuming. The more finely your tissue is ground, the more efficient you DNA extraction will be, making this a critical step for successful DNA extraction.

Phase Separation

A solution of phenol/chloroform/isoamyl alcohol is used to extract plant DNA from cellular debris and once added and vortexed, the mixture separates into three distinct phases: aqueous, interphase, and organic phase. While removing the aqueous phase and repeating the extraction is time consuming and laborious, it can also be challenging to remove all the aqueous phase, without disturbing the interphase. As a result, you may leave DNA behind or carryover contaminants from the interphase and organic phase, lowering your overall DNA yield and quality.

PCR Inhibitors

Several classes of biochemicals from plant tissues – polysaccharides, lipids, polyphenols, and/or other secondary metabolites – can coprecipitate with DNA, which can inhibit downstream applications that rely on thermostable DNA polymerases, such as PCR. The structure and concentration of these compounds can also vary substantially between different plant species, making the development and optimization of a “one size fits all” CTAB protocol difficult.^8,9 In addition, phenol and other salts introduced throughout your CTAB protocol can remain, even after extensive ethanol washes. These impurities can also interfere with downstream applications, including PCR and NGS.¹⁰

Zymo’s Alternative Method for Isolation of DNA From Plant Tissues

If that all seems like a bit much, you aren’t wrong. Happily, there are plant-specific DNA isolation kits which provide faster, more consistent, high-purity DNA extraction than the conventional CTAB protocols and variations thereof. These are essential for maintaining and further supporting the rapidly evolving pace, scope, and scale of agricultural R&D.

Zymo’s Quick-DNA Plant/Seed kits use bead beating and column-based purification to provide a simple, rapid workflow for the isolation of inhibitor-free DNA from a variety of plant sources (Figure 1). There are no repetitive and lengthy phase separation steps or hazardous reagents used, so you can further streamline your lab’s operations and protect the safety of key personnel. You can also skip the lengthy RNase digestion, incubation and centrifugation periods, and precipitation steps.

Figure 1. Our simple plant and seed DNA purification workflow is great for diverse sample types and delivers high-quality DNA for several downstream applications.

The DNA extraction protocol can be completed in as little as 15 minutes and will give you a straightforward path to high-quality DNA. If you’re working with a challenging plant species, such as cacao and cannabis, try out our state-of-the-art BashingBeads for more complete lysis and more consistent yields (Figure 2).^11-14

Figure 2. The Quick-DNA Plant/Seed kit delivers high-performance DNA from the most challenging plant species.

Our binding chemistry, wash solutions, and spin column technology remove polysaccharides, lipids, and other common downstream inhibitors and contaminants providing ultra-pure DNA, with minimal loss. Furthermore, our protocol has been optimized to work with a wide range of plant species and sample types, enabling novel and rapid advancements in modern plant genomics. See how we can help you extract high-quality plant DNA, in less time.

LEARN MORE ABOUT ZYMO’S PLANT DNA ISOLATION KITS HERE:

REFERENCES

Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead. IntechOpen website: https://www.intechopen.com/chapters/49877. Published July 14th, 2016. Accessed October 27th, 2021.
Doyle J, Doyle J. A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochem Bull. 1987;19(1):11-15.
Murray MG and Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic acids research. 1980; 8(19); 4321–4325. https://doi.org/10.1093/nar/8.19.4321
Aboul-Maaty NAF, Oraby HAS. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bull Natl Res Cent. 2019;43(25). doi.org/10.1186/s42269-019-0066-1
Muhammad I, Zhang T, Wang Y, et al. Modification of CTAB protocol for maize. Res J Biotech. 2013;8:41–45.
22. Safe Use of Phenol | Safety Services. UC – Davis Safety Services website: https://safetyservices.ucdavis.edu/safetynet/safe-use-of-phenol. Published March 26th, 2020. Accessed October 27th, 2021.
Report on Carcinogens, Fourteenth Edition. National Toxicology Program website: https://ntp.niehs.nih.gov/ntp/roc/content/profiles/chloroform.pdf. Published November 3rd, 2016. Accessed October 27, 2021.
Aboul-Maaty NAF, Oraby HAS. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bull Natl Res Cent. 2019;43(25). doi.org/10.1186/s42269-019-0066-1
CTAB Protocol for the Isolation of DNA from Plant Tissues. OPS Diagnostics website: https://opsdiagnostics.com/notes/protocols/ctab_protocol_for_plants.htm. Accessed October 27, 2021.
Angeles JGC, Laurena AC, Tecson-Mendoza EM. Extraction of genomic DNA from the lipid-, polysaccharide-, and polyphenol-rich coconut (Cocos nucifera L.). Plant Mol Biol Report. 2012;23(3):297-298. doi:10.1007/BF02772760
Kamber T, Malpica-López N, Messmer MM, et al. A qPCR Assay for the Fast Detection and Quantification of Colletotrichum lupini. Plants. 2021;10(8):1548. doi:10.3390/PLANTS10081548
Romero Navarro JA, Phillips-Mora W, Arciniegas-Leal A, et al. Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases. Front Plant Sci. 2017;8:1905. doi:10.3389/fpls.2017.01905
Cornejo OE, Yee MC, Dominguez V, et al. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process. Commun Biol. 2018;1:167. doi:10.1038/s42003-018-0168-6
Garfinkel AR, Otten M, Crawford S. SNP in Potentially Defunct Tetrahydrocannabinolic Acid Synthase Is a Marker for Cannabigerolic Acid Dominance in Cannabis sativa L. Genes. 2021;12(2):228. doi:10.3390/GENES12020228

February 9, 2022February 9, 2022

ARE SALIVA TESTS AS EFFECTIVE AS NASAL SWABS AT DETECTING COVID-19?

FIND OUT WHICH IS BEST FOR YOUR NEEDS

With COVID-19 cases rising and new variants emerging, demand for testing remains high. The persistent demand for COVID-19 tests has caused global shortages in swabs and personal protective equipment (PPE), which must be worn by those who collect swab samples. These shortages have forced public health officials to pivot towards alternative testing methods.^1,2 Although antigen tests, also known as “rapid tests,” are available, they have their drawbacks. Antibody detection from a blood sample cannot be used to detect active infections, and rapid antigen tests are generally not as sensitive as swab-based tests that use real time reverse transcription polymerase chain reaction (PCR) or other forms of nucleic acid amplification.^3,4 Saliva, by contrast, is gaining popularity as a swab alternative because it is easy to self-collect and less prone to supply chain disruptions. Yet one question remains: Are saliva tests as effective as nasal swabs at detecting COVID-19?

Considerations for Using Swab-based COVID-19 Tests

Swab-based testing is considered the gold standard for COVID-19 detection. Initially validated by the CDC as one of the first COVID-19 sample collecting methods, many people who have received a deep nasal (nasopharyngeal) swab remember the discomforting and invasive experience as one that “engender[s] visceral dislike,”⁵ causing fits of coughing, sneezing, and sometimes even a bloody nose. Deep nasal swabs are particularly uncomfortable and traumatizing for children. Although many online articles^6,7 offer solutions for parents wishing to get their children testing by nasal swab — from reassurance to bringing stuffed animals for emotional support — the idea of their child enduring such an irritating experience has caused many parents and patients to seek out a less invasive collection procedure or avoid being tested altogether.⁵

Allowing patients to self-collect nasal swabs can provide a sense of comfort and control. However, this approach comes with risks because patients can injure themselves or compromise the sample. Nose bleeding, retained foreign body, cerebrospinal fluid leak, and infection are all documented complications of nasal SARS-CoV-2 testing, although the former two are far more common than the latter two.⁸ Additionally, if self-collection instructions are unclear, patients can accidentally place swabs into the transport medium prior and then into their nose where the reagent may be harmful. Oral swabs and shallow nasal swabs, on the other hand, can be self-administered with fewer complications generally. These self-collected swabs may help to increase the bandwidth of testing for COVID-19.

For swab-based COVID-19 testing and other pathogen surveillance applications, safety and ease-of-use can be achieved through SafeCollect Swab Collection Kits. By containing DNA/RNA Shield, a DNA/RNA stabilization reagent, under a safety seal, this swab collection device minimizes user error and allows for unsupervised collection of both oral and shallow nasal swabs. After sample collection, the swab is plunged through the safety seal into the stabilization reagent; at this point, the sample can be stored at ambient temperatures kept at room temperature for up to 30 days. Customizable user instructions can also be created by Zymo Research for better compliance in unsupervised collection settings. With direct US-based manufacturing, production capacity can be customized for each order request, ensuring access to medical equipment regardless of global supply shortages.

Considerations for Using Saliva-Based COVID-19 Tests

For many, the most notable difference between saliva and swab-based sampling is the sample collection experience. By replacing invasive swabs with drooling in a tube, saliva-based sampling allows for effortless collection minus the nose bleeds and stuffed support animals.

With saliva-based collecting methods, patient care and satisfaction come first. The non-invasive procedure can be done unsupervised, resulting in higher compliance. Most saliva collection devices involve drooling or salivating saliva into a tube up to a fill line. In addition to being pain-free, saliva-based sampling is easier and safer than a nasal swab, making the method an attractive alternative for school testing programs, targeting a critical age group for pandemic surveillance.⁹ With saliva testing gaining FDA Emergency Use Authorization (EUA) and clearance from the CDC, is this alternative really as accurate and sensitive as swabs?

Multiple systematic analyses have compiled data from around the world comparing the accuracy and efficacy of saliva-based swab-based methods for the detection and diagnosis of SARS-CoV-2. Many have found that there is no significant difference between the two collection types, suggesting that saliva specimens may be preferred over nasal swabs due to their convenience and simplicity.^9-14

One meta-analysis compared the sensitivity and cost of swab and saliva-based testing. Not only did the researchers find comparable sensitivities between both methods for detection of SARS-CoV-2, but they estimated that collection of saliva-based samples instead of nasopharyngeal swabs would save an average $6.36 for every person tested. That figure quickly adds up in a pandemic where hundreds of thousands to millions of tests are administered daily.

Choosing the Right Saliva Collection Device

When determining the best saliva collection device for your specific application, several design characteristics and features should be considered. First, you can eliminate the need for cold storage and shipping by choosing a collection device that uses a nucleic acid stabilization reagent. Such devices not only minimize shipping and transportation costs but remove the chance of sample integrity loss from compromised storage conditions. Additionally, having a collection device with a stabilization solution already housed within ensures the highest quality of saliva is obtained and preserved from its immediate collection time until it’s tested. Finally, with at-home and unsupervised sample collection becoming increasingly common, saliva collection devices must be user-friendly and prioritize not only safety but consistent sampling as well.

The foolproof design of Zymo Research’s SafeCollect Saliva Collection Kit has several features that make for safe and streamlined saliva sample collection:

An easy-to-use collection funnel that simplifies the saliva sampling process
DNA/RNA Shield, a reagent that simultaneously inactivates pathogens and stabilizes nucleic acids in saliva for up to 30 days at ambient temperature
A safety seal that separates the your saliva sample from the DNA/RNA Shield reagent and unites the two only when the cap pierces the seal upon tightening

Fully customizable user-instructions can be designed and manufactured by our team to specifically fit your application needs, guaranteeing absolute transparency and consistency in your sample collecting process.

Swabs or saliva, Zymo Research’s products utilize a US-based manufacturer who directly controls their own supply chain, protecting its production capacity against shortages and guaranteeing fulfillment across all orders.

THE FUTURE OF SAFE SAMPLE COLLECTION

Sample collection was now completely unsupervised, increasing the probability of human error impacting sample quality. Most people have little to no sample collection experience, and the probability of accidents such as spilling stabilization solution or dipping swabs into the solution before swabbing their mouths increased. Ambient temperature aside, misuse in sample collection compromises the sample and jeopardizes patient health and test accuracy. The solution? Remove any type of interaction with the liquid stabilizer and sample until necessary.

SafeCollect Sample Collection Kits feature Zymo Research’s DNA/RNA Shield in a patented tube that prevents spillage, contact, and/or ingestion of the sample stabilization medium, combining user safety and consistent sampling together for a robust analysis with telehealth collection services. The patented SafeCollect Saliva and Swab Collection Kits have tubes that utilize a safety seal, only exposing your sample to the reagent once you’ve collected the sample and are ready to seal the tube. Samples collected at home are then shipped to a laboratory, where analysis can begin up to one month from collection date. In a time where everyone is still encouraged to minimize exposure by staying home as much as possible, the future of healthcare continues to progress and SafeCollect is but one solution to the ongoing efforts surrounding this pandemic.

LEARN MORE ABOUT ZYMO RESEARCH’S SALIVA AND SWAB COLLECTION DEVICES

REFERENCES

February 1, 2022February 1, 2022

Biolinkk is now an authorized distributor of ICHORBIO

Biolinkk is now an authorized distributor of ICHORBIO, Uk.

We have recently collaborated with a new company ICHORBIO based in Oxford (UK). ICHORBIO is supplier of research grade biosimilars and in vivo antibodies. They support in producing next Great oncology breakthrough. Part of the reason why cancer is so difficult to treat is because it is constantly mutating – and therefore the drugs they use must rapidly change and life science research must lead the way. They want to help your research to evolve as fast as cancer.

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