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NEWSLETTER

VOLUME 2, ISSUE 11 16 November 2013

2– 4 July 2014 RICT 2014: Interfacing Chem-ical Biology and Drug Discov-

ery. Venue: Rouen, France. 14– 17 July 2014

Course: Techniques & Appli-

cations of Molecular Biology.

Venue: Coventry, UK

3– 7 August 2014

13th International Confer-

ence on Bioinformatics.

Venue: Sydney, NSW, Aus-

tralia.

31 August– 4 September

2014

20th EuroQSAR Symposi-

um: Understanding Chemi-

cal-Biological Interactions.

Venue: St. Petersburg, Rus-

sia.

CONFERENCES

GENERAL NEWS Scientists developing techs to tackle low-quality rice (SciDev.net, October 2013)

Research is underway in Sub-Saharan Africa to develop nutritious rice varieties that are resistant to climate change, according to scientists who attended the Africa Rice Con-gress in Yaoundé, Cameroon, 21-24 October… Read more.

Who's afraid of peer review? (Science, October 2013)

A spoof paper, concocted by researcher Bohannon and submitted to selected open-access journals, achieved a startling acceptance rate. This has revealed a worrying prev-alence of predatory journals and little or no scrutiny at many of the open-access jour-nals… Read more.

Natural products discovery group asks for public's help with citizen science pro-

gram (Science daily, November 2013)

The University of Oklahoma Natural Products Discovery Group has taken an unconven-tional approach to finding new compounds with therapeutic relevance by launching a crowdsourcing initiative with citizen scientists from around the country… Read more.

Natural antibiotics target gram-negative pathogens (Drug Discovery and Develop-

ment, October 2013)

Scientists from Fundación Medina and Cubist Pharmaceuticals have discovered a new family of natural molecules that could serve as a scaffold to build next-generation antibiot-ics. These newly discovered molecules have unprecedented chemical structures and may address the emerging threat from Gram-negative pathogens... Read more.

UPCOMING BOOK PUBLICATION Adopted from Taylor & Francis Group

Herbal Drugs as Therapeutic Agents

To be published: January 2014

Phytochemicals are the mainstay of therapeutics of herbal or botanical medicine. Re-

search on phytomolecules is conducted worldwide and several have been screened for

clinical trials. This includes several promising anticancer phytomolecules, such as withaf-

erin-a and camphothecin. This book provides a scientific understanding of the mode of

action of these molecules. It targets only those phytochemicals and herbal extracts that

are subjects of recent pharmacological investigations. Chapters such as industrial crops

for steroid manufacturing and anticancer and cytotoxic potential of sesquiterpenoids add

special flavour to the book, making readers eager to learn more about the commercial

viability of phytochemical and herbal extracts.

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8th Regional Plant Biotechnology Forum

The ACGT’s 8

th Regional Plant Biotechnology Forum was presented on the 18

th of October, in partnership with Dr

Maretha O’Kennedy from the CSIR’s Biosciences Unit. The theme for the Forum was “Plant-Based Biologics”. The day saw 44 delegates convening at the CSIR’s Knowledge Commons in Pretoria. Attending delegates included individuals from higher education institutions, science councils, funding agencies as well as industry.

The keynote speaker for the forum, Dr Ann Meyers from the Uni-versity of Cape Town, gave a stimulating talk entitled: “Blue tongue virus-like particle vaccine candidate production in plants”. Dr Mey-ers’ main research interests are the expression of veterinary vac-cines and diagnostic reagents in plants and she is currently in-volved in projects including the production of such pharmaceuti-cals to target Rift Valley Fever virus, BTV and Crimean Congo haemorrhagic fever. Other speakers included Dr Tsepo Tsekoa (CSIR Biosciences), Mr Boet Weyers (OBP Vaccines), Dr Bridget Crampton (UP) and Ms Therese Stark on “Plant-based biologics at CSIR”. The forum was rounded off by Drs Tsepo Tsekoa and Michael Crampton giving

the delegates a tour of the CSIR’s Biomanufacturing Industry Development Centre (BIDC). The Forum gave delegates an insight into the current research initi-atives and capabilities at the various institutions, as well as the ca-pacity for downstream processing at the CSIR’s newly founded BIDC. Plans for the 9

th Regional Plant Biotechnology Forum are under-

way and the forum is expected to take place in March 2014 at the Agricultural Research Council in Pretoria. Keep an eye on the ACGT Events page for more information on the next plant forum. Suggestions regarding future topics and presenters can be sent to Thabo Khoza at TKhoza1@csir.co.za.

SABINA NEWS

Dr Tsepo Tsekoa giving a tour of the BIDC

Dr Ann Meyers presenting her work.

Annual RISE meeting

The annual rise meeting took place 25-26 October 2013, at the Aloe Ridge Hotel and Conference Centre near Johan-nesburg. The meeting was attended by a number of SABINA staff and students. Here’s what some of the attending students had to say about the meeting:

“The RISE meeting was a great experience for me. Being new in the organization, it allowed me to reconnect with old and meet new team members, who are already well versed in their field of work/expertise. It gave me a platform not only to get ideas on my own research but to also observe the level of output that is required for a member of the group and to clearly understand the importance of research as a way to improve solutions and solve challenges facing our continent. I am truly grateful to have been given the opportunity to attend such a gathering.” — Celine Mukakalisa “I met and chatted with people in the network whom I had never met before. The presentations from both current and

former students were very inspiring. I also liked the choice of the venue. It was very nice because it was not in town

and that’s what I would really want all the time. What I would like to see in future is that there should be a bit more

presentations from students mainly the current ones. Overall it was a very rewarding experience.” —Jimmy Sumani

“It was impressive to see how different networks (each comprising of people from different countries) come together to

work towards a common goal. The meeting also created an opportunity to meet members of other RISE networks.

Personally, I am impressed with how SABINA members know each other compared to other networks. The afternoon

session about students’ experiences and suggestions confirmed to me that not only I have benefited from the RISE-

SABINA but all others that are part of it have benefited as much as I did. Sithabile Tirivarombo’s experience at Duke

University was such an encouragement to apply for exchange programs in order to explore and experience life in oth-

er Institutions and the world. Thank you RISE and SABINA for the opportunity to be part of the meeting.” — Moola

Nyambe

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Beware of Predatory Publishers by Dr Carina van Zyl, CSIR Information Scientist, 8 November 2013

This time of the year is synonymous with Open Access (OA) awareness campaigns. However, you should also take note

of the strategies and tactics used by predatory publishers. The reality is that some of the OA articles reflected in the

VRE Newsletter are published in predatory journals. This does not mean that the articles are useless. It does mean that

you need to be more cautious before referencing and citing the article as the peer review process, in all probability, did

not take place prior to publication.

Predatory publishers use deception to appear legitimate, entrapping researchers into submitting their work and then

charging them to publish it. They exploit the author-pays model of open-access publishing for their own profit, spam pro-

fessional e-mail lists to solicit manuscripts and editorial board memberships, operate with a false-front or non-existent

peer review process and pay little attention to digital preservation.

Beall is synonymous with the drive against predatory publishers and maintains a list of culprits.

Initially in 2012 I agreed with researchers commenting in The Scientist that the problem is no-

where as serious as Beall asserts. However, the latest article by John Bohannon in Science,

“Who’s afraid of peer review?” (included above under “General News” and also see this NPR

commentary) provides evidence of a serious problem with respect to the quality of articles pub-

lished by predatory publishers. Bohannon wrote fake articles with scientific flaws and submitted

them for publication to 304 journals: 167 from Directory of Open Access Journals (DOAJ) , 121

from Beall's list and 16 listed by both. (DOAJ strives to be the credible list for OA journals, but

unfortunately one in every five publishers on Beall’s list is also on DOAJ.) Of the publishers on

Beall's list 82% accepted the articles, while 45% of publishers on DOAJ accepted the articles.

The question for researchers is: what could you do to protect yourself from these publishers? I would recommend that

before you publish in a journal, make sure the publisher is not on Beall's list of potential predatory OA publishers or

predatory standalone journals. Secondly one should be more aware of and familiar with the processes that good quality

journals follow. Make sure that claims regarding editorial boards, indexing, digital preservation, the stable of journals, the

impact factor and the peer review process, are true. Lastly, educate and familiarise yourself with Beall’s criteria for deter-

mining predatory publishers.

To further assist researchers we are also maintaining a list of publications on the topic of predatory publishers. Your as-

sistance in keeping the list up to date will be appreciated.

For enquiries: contact Carina at cvanzyl@csir.co.za.

SABINA NEWS

PhD graduation: Adushan Pillay

Congratulations to Adushan Pillay on his recent PhD graduation! We asked him to tell us about his research and share his experience as part of the SABINA network. We wish him all the best with his plans ahead!

My PhD thesis is titled “The Synthesis of the Quinones Dehydrohebarin, Anhydrofusarubin and the Acetal Core of Marticin” and it was supervised by Prof. C.B. de Koning and Dr. A.L. Rousseau. This work comprised the total synthesis of two natural products, of which the synthesis of anhydro-fusarubin was the first of its kind to be completed. Three publications were published from the work conducted in my PhD. Graduation was on the 4

th of July this year and it commemorated the end of my 8 years at Univer-

sity.

Being part of the SABINA network was a great experience and it allowed me to make new friends from neighbouring African countries and I was for-tunate enough to personally visit the Universities in Malawi and Namibia. The SABINA network also arranged several valuable training courses for us to attend and this did help with my professional development to some extent.

I am currently a postdoctoral associate at the South African Nuclear Energy Corporation and I design and synthesize cancer imaging agents. My future plan is to find a research position in medicinal chemistry.

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JOURNAL ARTICLES

Artemisia annua has a long tradition of use for the treatment of intermittent fevers which we now relate to malarial infections. The

active principle artemisinin has been isolated from Artemisia annua and today forms the backbone of the global fight against malaria.

The traditionally prepared Artemisia annua formulation is however still being used on a global scale for the treatment of malaria, and

it is claimed that its action is superior to the single purified drug. Artemisia annua is therefore on the forefront of the heated debate

between the single drug–single target approach of western based medicine and the holistic approach of traditional medicinal sys-

tems. This review aims to highlight the complexities we face in the general study of medicinal plants at the hand of three levels of

complexity. These levels consist of (a) the chemistry of the medicinal plant, (b) the influence of the preparation method on the chem-

istry of the final formulation and (c) the influence of metabolism on the chemistry of the formulation. We also provide an up-to-date

report on all scientific work that has been conducted and published in English on the traditional formulation of Artemisia annua. Very

little scientific work has been conducted on the Artemisia annua formulation. The available literature contains many discrepancies

which are unfortunately selectively being used by the two different sides in this debate to further their arguments. On one side of the

argument we have the low content of artemisinin in Artemisia annua, the low bioavailability of artemisinin when the traditional formu-

lation is administered and the high levels of recrudescence, which are being emphasised, while on the other side the possible role of

synergism and prodrugs are being highlighted. This review reports that there are still too many gaps in our existing knowledge to

provide conclusive evidence for either of the two sides of the argument.

The complexity of medicinal plants: The traditional Artemisia annua formulation, current status and future perspectives

Van der Kooy F, Sullivan SE, Journal of Ethnopharmacology, 150 (1), 1-13, 2013 35.95 USD (Link to article)

Indigenous knowledge is beginning to gain greater recognition in global discourse. The inability of western science to address the

myriad of illnesses facing mankind has extended the search for solutions into indigenous knowledge system, which was previously

dismissed as unreliable, and sometimes as mere superstitious. More and more western companies are beginning to explore and

patent indigenous knowledge of medicinal plants, roots, barks, nuts and seeds that are held by local communities. In Africa specifi-

cally, Western pharmaceutical companies are in a race to patent Africa's indigenous pharmacology, but without making the benefits

accruable to African indigenous communities and medicine men. The medications made from the indigenous knowledge of Africa's

medicinal plants are marketed globally; the huge profits generated from such sales are almost wholly retained by western business-

es. This paper explores the continued and increasing patenting and profiting from Africa's indigenous pharmacopeia by western

businesses. It calls for increased involvement of governments, civil society groups, concerned citizens and institutions in the protec-

tion of Africa's indigenous pharmacology, under a suitable framework.

Contending Issues of Intellectual Property Rights Protection and Indigenous Knowledge of Pharmacology in Africa South

of the Sahara

Ezeanya CA, Journal of Pan African Studies, 6 (5), 24-42, 2013 (Link to article)

The aim of the study was to determine the possible cytotoxicity of the aqueous stem bark extracts of Prunus africana and Warburgia

ugandensis to Vero E6 cells and acute toxicity in BALB/c mice. Despite being some of the most popular medicinal plants used in

Africa, little is known about their safety. In-vitro cytotoxicity tests on Vero E6 cells were investigated using MTT assay to assess the

safety of the two plant extracts. Vero E6 cells on growing to confluence were incubated with different drug concentrations for 48 h for

the drug to take effect. Viability of the cells was measured by a scanning multiwell spectrophotometer. In acute toxicity a total of 55

mice were used, divided into eleven groups of 5 mice; one group served as negative control and ten groups received oral gavage

doses at 500, 889.56, 1581.6, 2812.15 or 5000 mg/kg body weight once. Mortality and other signs of toxicity were recorded within

24 h and the weights of the surviving mice taken for 14 days thereafter. P. africana had CC50 of 104.08 μg/ml while W. uganden-

sis had CC50 > 250 μg/ml and both were classified as not cytotoxic. Lethal dose (LD50) for P. africana was 2201.207 mg/kg body

weight. W. ugandensis extracts had no mortality recorded in all dose levels and the LD50 was > 5000 mg/kg body weight. The

weights of mice that survived the entire 14 days in all groups increased and were not significantly different from that of con-

Safety of Prunus africana and Warburgia ugandensis in asthma treatment

Karani LW, Tolo FM, Karanja SM, Khayeka−Wandabwa C, South African Journal of Botany, 88, 183–190, 2013 35.95 USD (Link to article)

Ethanol extracts of Aloe ferox, Atalaya alata, Balanites maughamii, Clausena anisata, Croton menyaarthii,Lippia javanica, Melia

azedarach, Olax dissitiflora, Sclerocarya birrea and Trichilia emetica were evaluated for their larvicidal activity against Anopheles

arabiensis mosquitoes. Larval mortality was observed after 24 h of exposure. Larvicidal activity was only found in 5 plant extracts,

namely, C. anisata, C. menyaarthii, L. javanica, O. dissitiflora and T. emetica. The bark extract of O. dissitiflora exhibited the highest

larvicidal activity with LC50 value of 25.24 μg/ml. The results of the present study showed that the bark of O. dissitiflora may have the

potential to be used as larvicides against A. arabiensis.

Larvicidal activity against Anopheles arabiensis of 10 South African plants that are traditionally used as mosquito repel-

lents

Mavundza EJ, Maharaj R, Chukwujekwu JC, Finnie JF, Van Staden J, South African Journal of Botany, 88, 86-89, 2013

35.95 USD (Link to article)

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JOURNAL ARTICLES

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Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is

vital for drug discovery protocols. We assess the bioactivity and “drug-likeness” of a relatively small but structurally diverse dataset

(containing >1,000 compounds) from African medicinal plants, which have been tested and proven a wide range of biological activi-

ties. The geographical regions of collection of the medicinal plants cover the entire continent of Africa, based on data from literature

sources and information from traditional healers. For each isolated compound, the three dimensional (3D) structure has been used

to calculate physico-chemical properties used in the prediction of oral bioavailability on the basis of Lipinski’s “Rule of Five”. A com-

parative analysis has been carried out with the “drug-like”, “lead-like”, and “fragment-like” subsets, as well as with the Dictionary of

Natural Products. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Furthermore, de-

scriptors related to absorption, distribution, metabolism, excretion and toxicity (ADMET) have been used to predict the pharmacoki-

netic profile of the compounds within the dataset. Our results prove that drug discovery, beginning with natural products from the

African flora, could be highly promising. The 3D structures are available and could be useful for virtual screening and natural product

lead generation programs.

AfroDb: A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants

Ntie-Kang F, Zofou D, Babiaka SB, Meudom R, Scharfe M, Lifongo LL, Mbah JA, Mbaze LM,Sippl W, Efange SMN, PLoS ONE, 8 (10), e78085, 2013

Note: PLos ONE is an accredited OA journal with a good reputation. As always, use your discretion in assessing the quality of the research. (Link to article)

This study was done to identify random amplified polymorphic DNA (RAPD) markers that may associate with seven important traits

in tea. Sixty RAPD primers were first screened using 18 cultivars under each of the 7 traits, followed by confirmatory screening of 20

promising primers with 32 tea cultivars. Six RAPD primers generated a total of nine specific bands that associated with six desired

traits: black tea quality and tolerance to drought, high temperature, low temperature, Phomopsis theae, and high yield. These mark-

ers would allow early identification of plant material with the desired traits that can be advanced to the next stage of selection and

enhance targeted choice of breeding stocks with the desirable traits. The nine RAPD markers identified in this study could improve

precision and efficiency in tea breeding and selection and are an important contribution towards the establishment of marker-

assisted selection in tea breeding programmes.

Screening of Tea (Camellia sinensis) for Trait-Associated Molecular Markers

Mphangwe NIK, Vorster J, Steyn JM, Nyirenda HE, Taylor NJ, Apostolides Z, Applied Biochemistry and Biotechnology , 171 (2), 437-449, 2013

39.95 USD (Link to article)

Despite the popularity of traditional medicine in Africa, the continent remains behind in terms of the regulation, safety and quality

control of its medicinal plant industry. There is heightened interest in essential aspects that affect the industry, with storage practices

and consequent effects on plant efficacy being of high priority. Therefore, the effect of short-term storage on the efficacy and phyto-

chemical content of three popular medicinal plants (Ocimum basilicum, Senna petersiana and Hypoxis hemerocallidea) was investi-

gated. The antimicrobial and antioxidant activities of four solvent extracts of the selected plant (fresh and short-term stored) were

compared. Phytochemical analysis of 50% methanol extracts of plant materials was determined using spectrophotometric methods.

Fresh samples of the majority of the plant extracts indicated better antibacterial (Staphylococcus aureus and Escherichia coli) and

antifungal (Candida albicans) activities in comparison to the stored samples. There was no specific pattern in antioxidant activity for

both stored and fresh samples for the different plants. Phytochemical analysis pointed towards noticeable differences between fresh

and stored samples of the various plant extracts with fresh samples showing higher chemical concentrations in many plant parts. In

general, the current findings indicate that the degree of changes in the pharmacological and phytochemical activity due to storage

was plant part- and species-specific.

Evaluating the effect of storage on the biological activity and chemical composition of three South African medicinal plants

Laher F, Aremu AO, Van Staden J, Finnie JF, South African Journal of Botany, 88, 414-418, 2013 35.95 USD (Link to article)

The present study evaluates the hypoglycemic, antiperoxidative and antihyperlipidemic activities of saponins from Solanum an-

guivi fruits in alloxan induced diabetes rats. Diabetic rats were treated with saponin (20–100 mg/kg) for 21 days. Results indicated

that administration of saponins significantly reduced the elevated levels of glucose, decreased total cholesterol (TC), total triglycer-

ides (TG), low density lipoprotein (LDL) and increased high density lipoprotein (HDL) in the serum towards normalcy when compared

to the diabetic control (p < 0.05). In addition, saponins exhibited strong inhibition of lipid peroxidation and increased the levels of anti-

oxidant enzymes (superoxide dismutase and catalase) in the serum, liver and pancreas when compared to the diabetic control

(p < 0.05). Our results suggest that saponins from S. anguivi fruit can enhance the hypoglycemic, hypolipidemic and antioxidant

properties in alloxan-induced diabetic rats, and may have the potential to be used in the prevention or in the management of diabe-

Hypoglycemic, antiperoxidative and antihyperlipidemic effects of saponins from Solanum anguivi Lam. fruits in alloxan-

induced diabetic rats

Elekofehinti OO, Kamdem JP, Kade IJ, Rocha JBT, Adanlawo IG, South African Journal of Botany, 88, 56–61, 2013 35.95 USD (Link to article)