RESEARCH ARTICLE
Open Source Drug Discovery with the Malaria
Box Compound Collection for Neglected
Diseases and Beyond
Wesley C. Van Voorhis
1
*,JohnH.Adams
2
, Roberto Adelfio
3,4
, Vida Ahyong
5
,Myles
H. Akabas
6
, Pietro Alano
7
, Aintzane Alday
8
, Yesmalie Alemán Resto
9
, Aishah Alsibaee
10
,
Ainhoa Alzualde
8
, Katherine T. Andrews
11,12
, Simon V. Avery
13
, Vicky M. Avery
11
,
Lawrence Ayong
14
, Mark Baker
15
,StephenBaker
16,17,18
, Choukri Ben Mamoun
19
,
Sangeeta Bhatia
20
, Quentin Bickle
21
, Lotfi Bounaadja
22
, Tana Bowling
23
, Jürgen Bosch
24
,
Lauren E. Boucher
24
, Fabrice F. Boyom
25
, Jose Brea
26
,MarianBrennan
10
, Audrey Burton
23
,
Conor R. Caffrey
27
, Grazia Camarda
7
, Manuela Carrasquilla
28¤a
,DeeCarter
29
, Maria Belen
Cassera
30
, Ken Chih-Chien Cheng
31
, Worathad Chindaudomsate
32
, Anthony Chubb
10
,
Beatrice L. Colon
33
, Daisy D. Colón-López
24
, Yolanda Corbett
34
, Gregory J. Crowther
1
,
Noemi Cowan
3,4
, Sarah D’Alessandro
34
,NaLeDang
35
, Michael Delves
36
, Joseph L. DeRisi
5
,
Alan Y. Du
37
,SandraDuffy
11
, Shimaa Abd El-Salam El-Sayed
38,39
, Michael T. Ferdig
40
,
José A. Fernández Robledo
9
,DavidA.Fidock
41
, Isabelle Florent
22
, Patrick V. T. Fokou
25
,
Ani Galstian
42
, Francisco Javier Gamo
43
, Suzanne Gokool
44
,BenGold
45
, Todd Golub
42
,
Gregory M. Goldgof
46
, Rajarshi Guha
31
, W. Armand Guiguemde
47
, Nil Gural
20
,R.
Kiplin Guy
47
, Michael A. E. Hansen
14
, Kirsten K. Hanson
48,49
, Andrew Hemphill
50
,
Rob Hooft van Huijsduijnen
51
, Takaaki Horii
52
, Paul Horrocks
53
,TylerB.Hughes
35
,
Christopher Huston
54
,IkuoIgarashi
38
, Katrin Ingram-Sieber
3,4
, Maurice A. Itoe
49
,
Ajit Jadhav
31
, Amornrat Naranuntarat Jensen
55
, Laran T. Jensen
32
,RaysH.Y.Jiang
2
,
Annette Kaiser
56
, Jennifer Keiser
3,4
, Thomas Ketas
45
, Sebastien Kicka
57
, Sunyoung Kim
58
,
Kiaran Kirk
59
,VidyaP.Kumar
19
, Dennis E. Kyle
2
, Maria Jose Lafuente
43
, Scott Landfear
60
,
Nathan Lee
51
,SukjunLee
14
, Adele M. Lehane
59
,FengwuLi
60
,DavidLittle
45
, Liqiong Liu
58
,
Manuel Llinás
28
, Maria I. Loza
26
,AristeaLubar
61
, Leonardo Lucantoni
11
, Isabelle Lucet
62
,
Louis Maes
63
, Dalu Mancama
64
, Nuha R. Mansour
21
,SandraMarch
20
,SheenaMcGowan
65
,
Iset Medina Vera
49
, Stephan Meister
37
, Luke Mercer
23
, Jordi Mestres
66
, Alvine N. Mfopa
25
,
RajN.Misra
67
, Seunghyun Moon
14
,JohnP.Moore
45
, Francielly Morais Rodrigues da
Costa
68
,JoachimMüller
50
,ArantzaMuriana
8
, Stephen Nakazawa Hewitt
1
, Bakela Nare
23
,
Carl Nathan
45
, Nathalie Narraidoo
13
, Sujeevi Nawaratna
11,12
, Kayode K. Ojo
1
, Diana Ortiz
60
,
Gordana Panic
3,4
, George Papadatos
69
, Silvia Parapini
34
, Kailash Patra
61
, Ngoc Pham
11
,
Sarah Prats
43
, David M. Plouffe
70
, Sally-Ann Poulsen
11
, Anupam Pradhan
2
,CeliaQuevedo
8
,
Ronald J. Quinn
11
, Christopher A. Rice
2
, Mohamed Abdo Rizk
38,71
, Andrea Ruecker
36
,
Robert St. Onge
72
, Rafaela Salgado Ferreira
73
, Jasmeet Samra
28
, Natalie G. Robinett
24,74
,
Ulrich Schlecht
72
, Marjorie Schmitt
74
, Filipe Silva Villela
73
, Francesco Silvestrini
7
,
Robert Sinden
75
,DennisA.Smith
76
, Thierry Soldati
57
, Andreas Spitzmüller
66
,Serge
Maximilian Stamm
24
, David J. Sullivan
77
, William Sullivan
78
, Sundari Suresh
73
,
Brian M. Suzuki
27
,YoSuzuki
79
, S. Joshua Swamidass
36
, Donatella Taramelli
35
,
Lauve R. Y. Tchokouaha
25
, Anjo Theron
64
, David Thomas
42
, Kathryn F. Tonissen
11,80
,
Simon Townson
44
, Abhai K. Tripathi
77
, Valentin Trofimov
57
,KennethO.Udenze
2
,
Imran Ullah
53
, Cindy Vallieres
13
, Edgar Vigil
37
, Joseph M. Vinetz
61
, Phat Voong Vinh
16
,
Hoan Vu
11
,Nao-akiWatanabe
52
, Kate Weatherby
29
, Pamela M. White
78
,AndrewF.Wilks
81,82
,
Elizabeth A. Winzeler
37
, Edward Wojcik
58
,MelanieWree
37
,WesleyWu
5
, Naoaki Yokoyama
38
,
Paul H. A. Zollo
25
, Nada Abla
51
, Benjamin Blasco
51
, Jeremy Burrows
51
, Benoît Laleu
51
,
Didier Leroy
51
, Thomas Spangenberg
51¤b
, Timothy Wells
51
,PaulA.Willis
51
1 Departments of Medicine, Microbiology, and Global Health, Center for Emerging and Re-emerging
Infectious Diseases (CERID) University of Washington, Seattle, Washington, United States of America,
2 Center for Global Health and Infectious Diseases Research, Department of Global Health, University of
South Florida, Tampa, Florida, United States of America, 3 Medical Parasitology and Infection Biology,
PLOS Pathogens | DOI:10.1371/journal.ppat.1005763 July 28, 2016 1/23
a11111
OPEN ACCESS
Citation: Van Voorhis WC, Adams JH, Adelfio R,
Ahyong V, Akabas MH, Alano P, et al. (2016) Open
Source Drug Discovery with the Malaria
Box Compound Collection for Neglected Diseases
and Beyond. PLoS Pathog 12(7): e1005763.
doi:10.1371/journal.ppat.1005763
Editor: Margaret A Phillips, U Tex SouthWestern,
UNITED STATES
Received: April 1, 2016
Accepted: June 21, 2016
Published: July 28, 2016
Copyright: This is an open access article, free of all
copyright, and may be freely reproduced, distributed,
transmitted, modified, built upon, or otherwise used
by anyone for any lawful purpose. The work is made
available under the
Creative Commons CC0 public
domain dedication.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information files.
Much of the data also appears on ChemBL
https://
www.ebi.ac.uk/chembl/
Funding: Thanks to the UK DFID and the Bill and
Melinda Gates Foundation Grand Challenges
Explorations for providing funding for testing of the
Malaria Box and funding the support of individual
groups including: Medicines for Malaria Venture MMV
Challenge Grant, Grant Numbers MMV 12/0048 and
MMV 12/0076 (to JHA), the Australian Research
Council (FT10100185 to SAP; FT0991213 to KTA
Swiss Tropical and Public Health Institute, Basel, Switzerland, 4 University of Basel, Basel, Switzerland,
5 Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California,
San Francisco, California, United States of America, 6 Departments of Physiology & Biophysics,
Neuroscience and Medicine, Albert Einstein College of Medicine, New York, New York, United States of
America, 7 Dipartimento Malattie Infettive, Parassitarie ed Immunomediate Istituto Superiore di Sanità,
Roma, Italia, 8 BBD BioPhenix SL–BIOBIDE, Donostia, Gipuzkoa, Spain, 9 Bigelow Laboratory for Ocean
Sciences, East Boothbay, Maine, United States of America, 10 Molecular and Cellular Therapeutics, Royal
College of Surgeons in Ireland, Dublin, Ireland, 11 Eskitis Institute for Drug Discovery, Griffith University,
Nathan, QLD, Australia, 12 QIMR Berghofer Medical Research Institute Herston, Brisbane, Australia,
13 School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire, England, United
Kingdom, 14 Institut Pasteur Korea, Pangyo Techno-Valley, Gyeonggi Province, Korea, 15 Clinical
Pharmacology, Novartis Consumer Health, Nyon, Switzerland, 16 Oxford University Clinical Research Unit,
Wellcome Trust Major Overseas Programme, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam,
17 Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, Oxford University, Oxford,
England, United Kingdom, 18 The London School of Hygiene and Tropical Medicine, London, England,
United Kingdom, 19 Internal Medicine, Yale University, New Haven, Connecticut, United States of America,
20 Health Sciences and Technology/Institute for Medical Engineering and Science, Massachusetts Institute
of Technology, Cambridge, Massachusetts, United States of America, 21 Department of Immunology &
Infection, London School of Hygiene and Tropical Medicine, London, England, United Kingdom, 22 Museum
of National History, Sorbonne Universities, Paris, France, 23 SCYNEXIS, Inc., Durham, North Carolina,
United States of America, 24 Department of Biochemistry and Molecular Biology and Johns Hopkins Malaria
Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, Untied States of
America, 25 Department of Biochemistry, University of Yaoundé, Yaoundé, Cameroon, 26 CIMUS
Research Centre, University of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain,
27 Center for Discovery and Innovation in Parasitic Diseases, Department of Pathology, University of
California San Francisco, San Francisco, California, United States of America, 28 Department of
Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University,
University Park, Pennsylvania, United States of America, 29 School of Life and Environmental Sciences,
University of Sydney, Darlington New South Wales, Australia, 30 Department of Biochemistry and Virginia
Tech Center for Drug Discovery, Virginia Polytechnic Institute and State University, Blacksburg, Virginia,
United States of America, 31 National Center of Advancing Translational Sciences, NIH, Bethesda,
Maryland, United States of America, 32 Department of Biochemistry, Mahidol University, Bangkok, Thailand,
33 Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa,
Florida, United States of America, 34 Department of Pharmacological and Biomolecular Sciences, Università
degli Studi di Milano, Milano, Italy, 35 Department of Pathology and Immunology, Washington University in
St Louis, St. Louis, Missouri, United States of America, 36
Department of Life Sciences, Imperial College
London, London, England, United Kingdom, 37 Division of Pharmacology and Drug Discovery, Department
of Pediatrics, School of Medicine University of California San Diego, La Jolla, California, United States of
America, 38 National Research Center for Protozoan Diseases, Obihiro University of Agriculture and
Veterinary Medicine, Obihiro, Hokkaido, Japan, 39 Department of Biochemistry and Chemistry of nutrition,
Mansoura University, Mansoura City, Egypt, 40 Eck Institute for Global Health, Department of Biological
Sciences, University of Notre Dame, Notre Dame Indiana, United States of America, 41 Department of
Microbiology & Immunology and Division of Infectious Diseases, Department of Medicine, Columbia
University Medical Center, New York, New York, United States of America, 42 Broad Institute, Cambridge,
Massachusetts, United States of America, 43 Biochemistry and Parasitology Department, Malaria DPU,
Diseases of the Developing World (DDW), GlaxoSmithKline R&D, Tres Cantos, Madrid, Spain, 44 Tropical
Parasitic Diseases Unit, Northwick Park Institute for Medical Research, Harrow, Middlesex, England, United
Kingdom, 45 Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New
York, United States of America, 46 Medical Scientist Training Program, University of California, San Diego,
San Diego, California, United States of America, 47 Department of Chemical Biology & Therapeutics,
St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America, 48 Dept. of Biology
and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, San Antonio,
Texas, United States of America, 49 Instituto de Medicina Molecular, Lisboa, Portugal, 50 Institute of
Parasitology, University of Berne, Bern, Switzerland, 51 Medicines for Malaria Venture, Geneva,
Switzerland, 52 Global Health Research Section, hhc Data Creation Center, Eisai Co., Ltd, Tsukuba-shi,
Ibaraki, Japan, 53 Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire,
United Kingdom, 54 Department of Medicine, College of Medicine, University of Vermont, Burlington,
Vermont, United States of America, 55 Department of Pathobiology, Faculty of Science, Mahidol University,
Bangkok Thailand, 56 Medical Research Centre, Institute for Pharmacogenetics, Essen, Germany,
57 Department of Biochemistry, University of Geneva, Geneva, Switzerland, 58 Department of Biochemistry
and Molecular Biology, LSU Health Sciences Center, New Orleans, Louisiana, United States of America,
59 Research School of Biology, Australian National University, Canberra, Australian Capital Territory,
Australia, 60 Department of Molecular Microbiology & Immunology, Oregon Health & Science University,
Open Source Drug Discovery with the Malaria Box
PLOS Pathogens | DOI:10.1371/journal.ppat.1005763 July 28, 2016 2/23
and LP120200557 awarded to VMA), Bill & Melinda
Gates Foundation Grant OPP1040394 to PA,
OPP1040399 to DAF and VMA and OPP1086189 to
KKH, OPP1069393 and OPP1119049 to ML,
OPP1024029 to CN, the Bloomberg Family
Foundation (JBr), JHMRI for a predoctoral fellowship,
the US NIH for the CBI training grant T32GM080189
(to LEB), R01GM104486 (to PAW & WS),
R01AI117017 (to JHA) the National Science
Foundation Graduate Research Fellowship Program
Grant No.DGE-1232825 (DDCL), the South African
Medical Research Council Strategic Health
Innovation Partnerships (grant V6YBT51 to DM) and
the Council for Scientific and Industrial Research
(grant V1YTB95, to DM), and the French ANR
program Mammamia (ANR-12-BS07-0020-01). The
funders had no role in study design, data collection
and analysis, decision to publish, or preparation of
the manuscript.
Competing Interests: The following commercial
organizations employ or employed some of the
authors, which might be considered a conflict of
interest by some readers: BBD BioPhenix SL—
BIOBIDE: Aintzane Alday PhD, Ainhoa Alzualde
PhD, and, Arantza Muriana; Celia Quevedo PhD;
SCYNEXIS, Inc.: Tana Bowling, Audrey Burton, Luke
Mercer, and, Bakela Nare PhD; GlaxoSmithKline:
Francisco Javier Gamo, PhD, Maria Jose Lafuente,
PhD, and Sarah Prats; Eisai Co., Ltd.: Takaaki Horii
Ph.D. and Nao-aki Watanabe Ph.D.; Novartis Inc.:
Mark Baker PhD MSc (med), and David M. Plouffe;
Definiens AG: Andreas Spitzmüller PhD; and, Merck
Serono Inc: Thomas Spangenberg PhD.
Portland, Oregon, United States of America, 61 Department of Medicine, University of California San Diego,
San Diego, California, United States of America, 62 Department of Biochemistry and Molecular Biology,
Monash University, Clayton, Australia, 63 University of Antwerp, Department of Biomedical Sciences,
Antwerp, Belgium, 64 Biosciences Unit, Council for Scientific and Industrial Research, Pretoria, South Africa,
65 Department of Microbiology, Monash University, Clayton, Australia, 66 Chemotargets S.L. and Research
Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del
Mar Institute of Medical Research and University Pompeu Fabra, Barcelona, Catalonia, Spain, 67 Division of
Cancer Therapeutics and Diagnosis, Drug Synthesis and Chemistry Branch, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland, United States of America, 68 Graduate Program in
Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 69 ChEMBL
group, European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton,
Cambridgeshire, United Kingdom, 70 Genomics Institute of the Novartis Research Foundation, San Diego,
California, United States of America, 71 Department of Internal Medicine and Infectious Diseases, Faculty of
Veterinary Medicine, Mansoura University, Mansoura City, Egypt, 72 Department of Biochemistry and
Stanford Genome Technology Center, Stanford University, Palo Alto, Calilfornia, United States of America,
73 Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 74 Laboratoire de Chimie Moléculaire, CNRS,—UMR
7509, COB-IRJBD, Mulhouse Cedex, France, 75 The Jenner Institute, University of Oxford, Oxford, England,
United Kingdom, 76 Department of Chemistry, University of Capetown, Capetown, South Africa, 77 H.
Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health,
Baltimore, Maryland, United States of America, 78 Molecular, Cell and Developmental Biology, University of
California, Santa Cruz, Santa Cruz, California, United States of America, 79 Department of Synthetic Biology
and Bioenergy, J. Craig Venter Institute, La Jolla, California, United States of America, 80 School of Natural
Sciences, Griffith University, Nathan, Queensland, Australia, 81 Hudson Institute of Medical Research;
Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, 82 SYNthesis Research,
Parkville, Victoria, Australia
¤a Current address: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridgeshire, United Kingdom
¤b Current address: Global Health, Merck, Coinsins, Switzerland
*
wesley@uw.edu.
Abstract
A major cause of the paucity of new starting points for drug discovery is the lack of interac-
tion between academia and industry. Much of the global resource in biology is present in
universities, whereas the focus of medicinal chemistry is still largely within indus try. Open
source drug discovery, with sharing of information, is clearly a first step towards overcoming
this gap. But the interface cou ld especially be bridged through a scale-up of open sharing
of physical compounds, which would accelerate the finding of new starting points for drug
discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 com-
pounds representing families of structures identified in phenotypic screens of pharmaceuti-
cal and academic libraries against the Plasmodium falciparum malaria parasite. The set
has now been distributed to almost 200 research groups globally in the last two years, with
the only stipulation that information from the screens is deposited in the public domain. This
paper reports for the first time on 236 screens that have been carried out against the Malaria
Box and compares these results with 55 assays that were previously published, in a format
that allows a meta-analysis of the combined dataset. The combined biochemical and cellu-
lar assays presented here suggest mechanisms of action for 135 (34%) of the compounds
active in killing multiple life-cycle stages of the malaria parasite, including asexual blood,
liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds dem-
onstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 hel-
minths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the
Open Source Drug Discovery with the Malaria Box
PLOS Pathogens | DOI:10.1371/journal.ppat.1005763 July 28, 2016 3/23
NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmaco-
kinetic and metabolic properties were collected on all the compounds, assisting in the selec-
tion of the most promising candidates for murine proof-of-concept experiments and
medicinal chemistry programs. The data for all of these assays are presented and analyzed
to show how outstanding leads for many indications can be selected. These results reveal
the imme nse potential for translating the dispersed expertise in biological assays inv olving
human pathogens into drug discovery starting points, by providing open access to new fam-
ilies of molecules, and emphasize how a small additional investment made to help acquire
and distribute compounds, and sharing the data, can catalyze drug discover y for dozens of
different indications. Another lesson is that when multiple screens from different groups are
run on the same library, results can be integrated quickly to select the most valuable starting
points for subsequent medicinal chemistry efforts.
Author Summary
Malaria leads to the loss of over 440,000 lives annually; accelerating research to discover
new candidate drugs is a priority. Medic ines for Malaria Venture (MMV) has distilled
over 25,000 compounds that kill malaria parasites in vitro into a group of 400 representa-
tive compounds, called the "Malaria Box". These Malaria Box sets were distributed free-of-
charge to research laboratories in 30 differe nt countries that work on a wide variety of
pathogens. Fifty-five groups comp iled >290 assay results for this paper describing the
many activities of the Malaria Box compounds. The collective results suggest a potential
mechanism of action for over 130 compounds against malaria and illuminate the most
promising compounds for further malaria drug development research. Excitingly some of
these compounds also showed outstanding activity against other disease agents including
fungi, bacteria, other single-cellular parasites, worms, and even human cancer cells. The
results have ignited over 30 drug development programs for a variety of diseases. This
open access effort was so successful that MMV has begun to distribute another set of com-
pounds with initial activity against a wider range of infectious agents that are of public
health concern, called the Pathogen Box, available now to scientific labs all over the world
(
www.PathogenBox.org).
Introduction
Preclinical development for drugs in neglected diseases remains a slow process due to a lack of
access to compounds, and legal complications over intellectual property ownership. One way to
accelerate drug discovery is to provide open access to bioactive molecules with public disclosure
of the resulting biological data. The data from open access of bioactive molecules can help priori-
tize which compounds to investigate further through medicinal chemistry for the original indica-
tion and can also uncover other indications for compound development. It was in this spirit of
providing open access of malaria-bioactive compounds, and disseminating the results in the pub-
lic domain, that the Malaria Box project was initiated by the Medicines for Malaria Venture.
Origins of the ‘Malaria Box’ compound set
Since 2007, over 6 million compounds were screened against asexual-stage Plasmodium falcip-
arum, at two pharmaceutical companies (GlaxoSmithKline [
1] and Novartis [2]), and two
Open Source Drug Discovery with the Malaria Box
PLOS Pathogens | DOI:10.1371/journal.ppat.1005763 July 28, 2016 4/23
academic centers (St. Jude, Memphis [3], and Eskitis, Australia [4]), resulting in over 20,000
compounds active in the low- to sub-micromolar range. The structures of the 20,000 anti-
malaria hits were made available in ChEMBL (
www.ebi.ac.uk/chembl), but discussions with
biology groups had underlined the importance of access to the compounds themselves for test-
ing. Cluster analysis and commercial availability reduced this to a set of 400 representative
compounds, the ‘Malaria Box’, which was distributed freely to researchers who provided a
rationale for screening [
5]. This paper presents a summary and analysis of the collected results
of the Malaria Box screening from 55 groups who performed a wide variety of assays, the large
majority of which are presented in this paper. The collective results are greater than the sum of
the individual assays, because each compound can be queried for activity, pharmacokinetic,
and safety data to gauge its suitability as a starting point for subsequent medicinal chemistry
optimization efforts.
Results
The Heat Map (S1 Table) reports the data from over 290 assays run on the Malaria
Box compounds; a snapshot is shown in
Fig 1. The results are color coded, where the com-
pounds with the highest activity are coded red and those with relative inactivity green. In the
center of the box in
S1 Table, the numerical value for the compound is given. It can be seen
immediately that some compounds have activities in several biological assays across multiple
species and these tend to have activity against mammalian cells as well, whereas other com-
pounds have a rather limited spectrum of activity and are less toxic to mammalian cells.
The data demonstrated in
S1 Table are provided by 55 groups who have performed 291
assays to screen the Malaria Box. The vast majority of the data are presented for the first time
in this paper. In supplementary data
S1 Table, note that columns with data presented for the
first time in this paper, representing 236 assays, are colored pink on the top row; published /in
press data columns, 55, are grey, with citations provided. Presenting the combined dataset pro-
vides insights into the hit rates in these various assays while allowing rapid access to the data
by the wider scientific community.
The Heat Map (
S1 Table) presents the Malaria Box chemicals grouped by chemical related-
ness. Of the 400 compounds, over 100 are closely-related paired molecules so immediate struc-
ture-activity-relationships (SAR ) can often be seen from hits with these pairs. The Heat Map
identified obvious correlations in chemistry and biology between compounds (both Mecha-
nism-of-Action and phenotypic activity). Some biological assays are relatively similar; for
example, there were a large number of different P . falciparum gametocyte assays (
S1 Table, col-
umns AV-CB), which also cluster, although not perfectly. As such, the aggregate screening
data help overcome inter-laboratory bias and identify outstanding activities. For example, com-
pounds that were active in multiple gametocyte assays represent more solid positives than a
compound that was active in only one screening assa y. However, the gametocyte assays were
often performed using different techniques and screening concentrations (see
S1 Methods and
Results
, for details) and one assay may be preferred over another to select compounds with
gametocyte activity. Thus having the aggrega te data presented together with the individual pro-
tocols is more valuable than just having each individual data set to look at sequentially.
Malaria Box safety and pharmacokinetic data
Early safety data were obtained by testing all compounds against 73 human cell lines at 10 μM
or above, and developing zebrafish embryos were exposed at 5 μM, providing furt her clues on
potential safety issues. A frequent cardiotoxicity safety concern is QTc prolongation, and all
compounds were screened for hERG inhibition [
6], which is a proxy for this risk (S1 Table
Open Source Drug Discovery with the Malaria Box
PLOS Pathogens | DOI:10.1371/journal.ppat.1005763 July 28, 2016 5/23