Final Program
Speakers
Gunda I. Georg
Director, Institute for Therapeutics Discovery and Development
University of Minnesota, USA
Editor-in-Chief for the Journal of Medicinal Chemistry
Dr. Georg is Regents Professor and Head of the Department of Medicinal Chemistry and the founding Director of the Institute for Therapeutics Discovery and Development (ITDD) at the University of Minnesota College of Pharmacy. She holds the Robert Vince Endowed Chair and the McKnight Presidential Chair in Medicinal Chemistry. She is Editor-in-Chief for the Journal of Medicinal Chemistry. She was elected to the American Chemical Society Medicinal Chemistry Hall of Fame in 2017. She is an AAAS Fellow, a Fellow of the American Chemical Society, and has received the Ernest H. Volwiler Research Achievement Award of the American Association of Colleges of Pharmacy, the Sato Memorial International Award of the Pharmaceutical Society of Japan, the University of Minnesota Academy for Excellence in Health Research, and others.
Dr. Georg received a BS in pharmacy (1975) and a PhD degree in medicinal chemistry (1980) from Philipps University in Marburg, Germany. She was a postdoctoral fellow in the Department of Chemistry at the University of Ottawa in Canada. She started her independent career at the University of Kanas in 1984. She joined the University of Minnesota in 2007. Her research focuses on the design, synthesis, and evaluation of biologically active agents. Current major therapeutic areas are focused on cancer and male contraception.
Dr. Georg’s work is described in over 230 publications. She has trained more than 100 PhD and post-doctoral students, most of whom have pursued careers in the pharmaceutical industry. She is actively involved in professional organizations including the American Chemical Society and the AAAS. She has served for many years as grant reviewer on NIH study sections, for the NSF, AAAS, foundations and universities. She is a member of advisory boards for several scientific journals and universities.
Drug Discovery in Academia: The Institute for Therapeutics Discovery and Development at the University of Minnesota, USA
The presentation will describe the organization of the Institute and its successes in patenting and licensing three clinical candidates for cancer chemotherapy, epileptic seizures and glaucoma treatment.
Aled Edwards
CEO, Structural Genomics Consortium (SGC)
University of Toronto, Canada
Dr. Aled Edwards is founding and current CEO of the Structural Genomics Consortium (SGC), Professor at the University of Toronto and Visiting Professor at the University of Oxford. Trained as a protein biochemist at McGill University (with Peter Braun) and at Stanford University (with Roger Kornberg), his research interests include structural biology, host-virus interaction, functional proteomics and drug discovery. In 1997, he and Dr. Cheryl Arrowsmith, contemporaneously with others around the world, launched a pilot project in structural genomics. The publication of their pilot project represented the first report of a large-scale effort in structural biology. Since 2000, Al and his colleagues have contributed to over 2,000 unique protein structures into the Protein Data Bank. Al’s other interests include open access and open innovation approaches to drug discovery, and science outreach.
Open Source Drug Discovery for Kids Rare Diseases
A. Ganesan
University of East Anglia, UK
Ganesan obtained a BSc (Hons) in Chemistry at the National University of Singapore (1986). He completed his PhD in synthetic methodology and total synthesis under the supervision of Clayton Heathcock at the Department of Chemistry, University of California-Berkeley (1992) and was subsequently a postdoctoral fellow with Gregory Verdine at the Department of Chemistry at Harvard University. In 1993, he joined the Institute of Molecular and Cell Biology in Singapore as a Senior Research Chemist at the Centre for Natural Product Research and in 1996 became Principal Investigator of the Institute’s Medicinal and Combinatorial Chemistry group. In 1999 he joined the University of Southampton as a Reader in the Combinatorial Chemistry Centre for Excellence. In 2011 he became the Chair of Chemical Biology at UEA’s School of Pharmacy. He is Director of Postgraduate Research and Head of the Healthy Ageing research theme within the School. Ganesan is co-founder of the biotech company Karus Therapeutics and Chair of the EU COST Action CM1406, ‘Epigenetic Chemical Biology’. He sits on the IUPAC Subcommittee for Medicinal Chemistry and Drug Development and the Royal Society of Chemistry’s Bioorganic & Medicinal Chemistry Sector committee. Ganesan’s research centres around chemical biology, medicinal chemistry and organic synthesis with an emphasis on biologically active natural products and epigenetics.
Heavy metal fans: Targeting the zinc-dependent histone deacetylases (HDACs)
The human genome encodes for a relatively modest proteome (~20,000 proteins). However, this number is exponentially expanded through post-translational modifications (PTMs), among which the second most prevalent after phosphorylation is the acetylation of lysine residues.
Lysine acetylation is reversible, being dynamically removed by the action of sirtuin and zinc-dependent histone deacetylase (HDAC) enzymes. Five HDAC inhibitors are now clinically approved as anticancer agents and they work primarily by occupying the substrate binding pocket through reversible coordination with the active site zinc cation. In this presentation, I will summarise the current progress with HDAC inhibition, highlighting recent developments with isoform selectivity and their therapeutic potential. I will give examples of HDAC inhibitors from our group arising from natural products as well as synthetic compounds.
Reviews
• Ganesan, A. Epigenetic Drug Discovery: A Success Story for Cofactor Interference. Phil. Trans. R. Soc. B 2018, 373, 20170069.
• Ganesan, A. Multitarget Drugs: an Epigenetic Epiphany. ChemMedChem 2016, 11, 1227-1241.
• Ganesan, A. Macrocyclic Inhibitors of Zinc-dependent Histone Deacetylases (HDACs). In Macrocycles in Drug Discovery; Levin, J., Ed. RSC, Cambridge, 2015, 109-140.
Recent HDAC Publications
• Ruzic, D.; Petkovic, M.; Agbaba, D.; Ganesan, A.; Nikolic, K. Combined Ligand and Fragment‐based Drug Design of Selective Histone Deacetylase–6 Inhibitors. Mol. Informatics 2019, 38, 1800083.
• Lecointre, B.; Narozny, R.; Borrello, M. T.; Senger, J.; Chakrabarti, A.; Jung, M.; Marek, M.; Romier, C.; Melesina, J.; Sippl, W.; Bischoff, L.; Ganesan, A. Isoform-selective HDAC1/6/8 Inhibitors with an Imidazo-ketopiperazine Cap Containing Stereochemical Diversity. Phil. Trans. R. Soc. B 2018, 373, 20170364.
• Conforti, F.; Davies, E. R.; Calderwood, C. J.; Thatcher, T. H.; Jones, M. G.; Smart, D. E.; Mahajan, S.; Alzetani, A.; Havelock, T.; Maher, T.; Molyneaux, P. L.; Thorley, A. J.; Tetley, T. D.; Warner, J. A.; Packham, G.; Ganesan, A.; Skipp, P. J.; Marshall, B. J.; Richeldi, L.; Sime, P. J.; O’Reilly, K. M. A.; Davies, D. E. The Histone Deacetylase Inhibitor, Romidepsin, as a Potential Treatment for Pulmonary Fibrosis. Oncotarget 2017, 8, 48737-48754.
• Liu, Q.; Lu, W.; Ma, M.; Liao, J.; Ganesan, A.; Hu, Y.; Wen, S.; Huang, P.; Synthesis and Biological Evaluation of Santacruzamate A and Analogs as Potential Anticancer Agents. RSC Adv. 2015, 5, 1109-1112.
• Benelkebir, H.; Donlevy, A. M.; Packham, G.; Ganesan, A. Total Synthesis and Stereochemical Assignment of Burkholdac B, a Depsipeptide HDAC Inhibitor. Org. Lett. 2011, 13, 6334-6337.
• Benelkebir, H.; Marie, S.; Hayden, A.; Lyle, J.; Loadman, P.; Crabb, S. J.; Packham, G.; Ganesan, A. Total Synthesis of Largazole and Analogues: HDAC Inhibition, Antiproliferative Activity and Metabolic Stability. Bioorg. Med. Chem. 2011, 19, 3650-3658.
• Tiffon, C. E.; Adams, J. E.; van der Fits, L.; Wen, S.; Townsend, P. A.; Ganesan, A.; Hodges, E.; Vermeer, M. H.; Packham, G. The Histone Deacetylase Inhibitors Vorinostat and Romidepsin Downmodulate IL-10 Expression in Cutaneous T-cell Lymphoma Cells. Br. J. Pharmacol. 2011, 162, 1590-1602.
• Wen, S.; Packham, G.; Ganesan, A. Macrolactamization versus Macrolactonization: A Practical Total Synthesis of FK228, the Depsipeptide Histone Deacetylase Inhibitor. J. Org. Chem. 2008, 73, 9353-9361.
Carlos Alberto Manssour Fraga
LASSBio, Institute of Biomedical Sciences, Federal University of Rio de Janeiro,Brazil
Carlos Alberto Manssour Fraga obtained a B.Sc. degree in Pharmacy in 1988 and his M.Sc. degree in Sciences (Medicinal Chemistry) from Federal University of Rio de Janeiro (UFRJ). After obtaining his Ph.D. degree from Chemistry Institute of UFRJ in 1994, working with the synthesis of novel stable prostacyclin mimetics under the supervision of Professor Eliezer J. Barreiro, Carlos Alberto Manssour Fraga joined the Faculty of Pharmacy of UFRJ (Rio de Janeiro) as Assistant Professor in 1996 and was promoted to Associate Professor in May 2006. Then, Professor Fraga moved to Institute of Biomedical Sciences, where in 2012 he became Full Professor. He was the Coordinator of the Post Graduate Program in Pharmacology and Medicinal Chemistry of the Institute of Biomedical Sciences from 2011 to 2015 and currently he occupies the position of Director of Research. Dr. Fraga is an effective member of Brazilian Chemical Society since 1991, where he was Director of the Medicinal Chemistry Division from 2002 to 2004. Apart from teaching, Professor Fraga develops his research activities in LASSBio (Laboratório de Avaliação e Síntese de Substâncias Bioativas at UFRJ, www.lassbio.icb.ufrj.br ), focusing the design, synthesis, and pharmacological evaluation of novel drug candidates able to act in multifactorial diseases, with particular emphasis in the use of N-acylhydrazone framework as a privileged structure to discover novel therapeutically valuable compounds.
Discovery of Novel Kinase Inhibitors Belonging to Isosteric N-Acylhydrazone or N-Sulfonylhydrazone Classes
The growing impact of inflammatory chronic-degenerative diseases able to affecting different tissues/organs such as the articulations (e.g. rheumatoid arthritis), the bowel (e.g. Chron’s disease), the blood vessels (e.g. pulmonary hypertension, cerebral cavernous malformation), the metabolic behavior (e.g. diabetes mellitus) and also different types of cancer has led to the emerging necessity of discovering novel drug candidates useful to treating these multifactorial diseases. Since the complete characterization of the human genome, the protein kinases were identified as one of the main group of druggable enzymes. However, a number relatively reduced of kinases has been still exploited as drug targets. This kind of proteins play a central role in signal transduction, being related to other important processes like the control of cell cycle, proliferation, differentiation, mobility and mechanisms related to survival or cell death. Many of these processes regulated by kinases actions are related to the pathogenesis of chronic multifactorial diseases. In our research group, i.e. LASSBio-UFRJ, we have successfully exploited the N-acylhydrazone1 (NAH) framework as a privileged structure2 to the identification of compounds able to be selectively recognized by different biotargets, such as adenosine A2A receptors, PDE-4 and HDAC6 enzymes, among others. This peptidomimetic framework, which is resultant from the fusion between amide and imine subunits, is able to provide points of interaction with a wide range of amino acid residues, comprising both H-bond acceptor and donor sites. So, this lecture describes our efforts to found out novel inhibitors of some serine-threonine kinases, such as IKKb, p38, ROCK and GSK-3b, and tyrosine kinases (PI3Ka) belonging to N-acylhydrazone or isosteric N-sulfonylhydrazone classes applying different strategies of molecular modification.3-6
Acknowledgements
Thanks are due to INCT-INOFAR (BR), CNPq (BR), CAPES (BR), DECIT-MS (BR) and also to FAPERJ (BR) for the financial support and fellowships.
References
1 Thota, S. et al. (2018) Bioorg. Med. Chem. Lett., 28, 2797; 2Duarte, C. D. et al. (2007) Mini Rev. Med. Chem., 7, 1108; 3 Avila, C. M. (2011) Eur. J. Med. Chem., 46, 1245; 4 Guedes, I. A. et al. (2015) ChemMedChem, 11, 234; 5Oliveira, R. G et al. (2018) J. Enz. Inhib. Med. Chem., 33, 1181; 6 Tesch, R. et al. (2018) Angew. Chem. Int. Ed., 57, 9970.
Chung Man Chin
University of Sao Paulo State, Araraquara, Brazil
Chung Man Chin is Associate Professor at School of Pharmaceutical Sciences, University of Sao Paulo State (UNESP), Araraquara, SP and is coordinator of Lapdesf -Laboratory of Drug Design. The research interests includes drug design of new drugs for neglected diseases, sickle cell anemia, anti-inflammatory and anticancer compounds.
Design, Synthesis and Biological evaluation for the discovery of drug candidates for Sickle Cell Disease
Sickle cell disease (SCD) is a chronic hereditary hemolytic anemia characterized by a single nucleotide mutation (GTG to GAG) in the sixth codon of the gene encoding β-globin, causing the replacement of glutamic acid with a valine residue in the protein forming the β-globin chain. The main clinical symptoms of SCD include chronic inflammation, vasculopathy, microvascular vaso-occlusion and acute/chronic multiorgan damage. The only drug in current therapy is the hydroxyurea (HU) that is able to increase fetal hemoglobin (HbF). Even though the toxicity, the use of HU is associated with decreased morbidity and mortality in SCA patients, however, not all respond to or tolerate to HU which provides a rationale for the development of novel HbF inducers as treatment options for SCA. We will show the results obtained by Lapdesf Researcher Group (UNESP, Araraquara, SP, Br) in the last 10 years efforts to obtain a novel approach for treating sickle cell disease symptoms. The molecular hybridization was the main tool used to design new compounds of hydroxyurea (HU) and NO donors (N-oxide) with thalidomide analogs or phtalimide derivatives. The results demonstrated compounds with the ability not only to increase HbF production (g-globin expression) in transgenic SCA mouse model but also with the capable to reduces the production of pro-inflammatory cytokines by SCA mouse monocytes cultured ex vivowithout genotoxic or mutagenic using CHO-K1 cells. The g-globin increase of phenylsulfonylfuroxan derivatives are related to the induction of the acetylation of histones H3 and H4. In summary, the non genotoxic N-oxide phtalimide hybrid derivatives represents a promising new canditates for SCD treatmentthat areable to induce g-globin expression and also present the analgesic and antiplatelet activity, TNF-alpha inhibition effect, beneficial activities to decrease patients suffering.
Daniel Bargieri
Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
Searching for new malaria transmission-blocking compounds
The lack of drugs that effectively block malaria transmission is a major obstacle for malaria elimination efforts, thus The WHO Global Technical Strategy for Malaria 2016-2030 includes a call for the discovery and development of new drugs active against Plasmodium sexual stages, the gametocytes, which are the parasite forms infective to the mosquito vector. In response, gametocyte viability assays were developed and several small molecule libraries screened, but only yielded a small number of good options for further development. To extend the screen to include all the events triggered immediately after gametocytes are taken up in a blood meal by a mosquito, we developed and validated a P. berghei (rodent malaria) Nanoluciferase (nLuc)-based fertilization reporter line. When the gametocytes arrive in the mosquito they activate to form gametes, which fertilize and form a zygote. The new reporter line is able to assess gametocyte activation and gamete fertilization in high-throughput. The development of the reporter line and compound screens will be presented.
Elizabeth Bilsland
Assistant professor – Department of Structural and Functional Biology, Institute of Biology , State University of Campinas (UNICAMP), Brazil
Elizabeth Bilsland is assistant professor in the Department of Structural and Functional Biology, Institute of Biology, UNICAMP. Graduated in Agronomic Engineering at ESALQ, USP (1995), has a PhD in Cell and Molecular Biology – Göteborg University, Sweden (2004 ) and post- doctorate in Biochemistry at the University of Cambridge ( United Kingdom – 2004 to 2015 ) . Has experience in genetics and biochemistry with emphasis on synthetic biology. Uses Saccharomyces cerevisiae as a platform for the discovery of new drugs. This includes the genetic engineering of various metabolic pathways of the yeast for screenings on a large scale. Develops modulators of heterologous metabolic pathways in yeast works on the identification of new compounds with antiparasitic activity, performs chemical-genomic profiling for the indentification of mode of action of natural compounds with antiviral, antibacterial or antiparasitic activity, and works on the identification of cellular drug import mechanisms.
The transporter-mediated uptake of drugs is the rule
Traditionally, drugs have been designed based on the assumption that they enter cells through passive diffusion through the plasma membrane lipid bilayer. However, a growing body of evidence is emerging showing that passive diffusion via lipid bilayer is an exception and not the rule. We have constructed a library of over 14000 Saccharomyces cerevisiae strains with deletions in pairs of genes encoding non-essential plasma membrane transporters and provide compelling evidence that drugs enter cells primarily through proteinaceus transmembrane carriers.
Eufrânio N. da Silva Júnior
Federal University of Minas Gerais, Brazil
Eufrânio N. da Silva Júnior obtained his PhD in Chemistry at the University of Brasília in 2009. In 2010, he started his independent career as Professor at the Federal University of Minas Gerais (UFMG). He is a member of the SBQ and RSC. His recent awards and distinctions include RSC/BMOS Young Investigator Award (2015), Jones Travelling Fellowship (visiting professor at Bristol University – UK, 2016), MedChemComm New Talent: Americas (2017), Themed collection ‘Contributors to the emerging investigators issue 2018’ of Chemical Society Reviews, and Capes-Humboldt Research Fellowship for experienced researchers (2018). Currently, he is visiting Professor at Universität Göttingen – Georg-August-Universität Göttingen – Germany hosted by Prof. Lutz. Ackermann. His research interests are focused on C-H bond activation reactions, organocatalysis, mechanistic investigations, click chemistry and synthesis of heterocyclic and naphthoquinoidal bioactive and fluorescent compounds. He has 85 publications related to Organic Chemistry and Medicinal Chemistry.
Exploring different facets of catalysis towards bioactive quinoidal compounds: The complexity of simple and powerful molecules
Our group has developed practical methods for design, synthesize and optimize new heterocyclic compounds with a broad range of biological applications. In this context, we revealed the synthesis and biological evaluations (e.g. bioimaging, cellular uptake and dynamics in living cells) of new fluorescent heterocyclic compounds, which have allowed visualizing the whole endocytic pathway and selective cellular staining of lipid-based structures, that is, lipid inclusions in the cytosol. In addition, modular synthesis via organocatalysis of diverse naphthoquinones and selenium-containing quinone-based triazoles possessing two redox centres, with trypanocidal and antitumor activities were recently described by our group. This lecture will present a combination of strategies in Medicinal Chemistry and synthetic methodologies, as for instance, transition metal catalysed C-H activation for the synthesis of bioactive compounds and combination of aryl diselenides/hydrogen peroxide and carbon nanotube/rhodium nanohybrids for naphthol oxidation and preparation of trypanocidal quinones. The development of reactions that produces in a single step highly antitumor and trypanocidal naphthoquinoidal compounds will be presented, along with recently developed iodination, oxygenation, thiolation and selenation processes. Strategies and reactions to prepare fluorescent compounds used to monitor enzymatic processes will also be briefly discussed.
Glaucius Oliva
Center for Research and Innovation in Biodiversity and Drug Discovery(CIBFar/CEPID)Institute of Physics of São Carlos, University of São Paulo, Brazil.
GLAUCIUS OLIVA is Senior Professor at the Institute of Physics of São Carlos, University of São Paulo. He obtained his PhD in Protein Crystallography and Structural Biology at the University of London in 1988. He was the key leader in the establishment of Protein Crystallography research in Brazil, including the development of the first protein crystallography beamline at the Brazilian National Synchrotron Laboratory. He was an International Scholar of the Howard Hughes Medical Institute (1997-2001) and is Member of the Brazilian Academy of Sciences, The World Academy of Sciences (TWAS), the Academy of Sciences of Latin America (ACAL) and holder of the Grã-Cruz Medal of the National Order of Scientific Merit of Brazil. He served as President of the Brazilian National Council for Scientific and Technological Development-CNPq (2011-2015). His scientific interests are focused on Macromolecular Structure Determination by X-ray Crystallography, Structure-Based Drug Design, Medicinal Chemistry, Tropical Infectious Diseases (Chagas, leishmaniasis, malaria), Biotechnology, Cancer, Tubulin, Arboviruses, Zika virus, Yellow Fever virus, Chikungunya virus.
Collaborative research and innovation in drug discovery against arboviruses circulating in Brazil
We will describe our structural biology studies of arboviral proteins, including the crystallographic structures of Zika virusNS5 RNA-dependent RNA polymerase and NS3-helicase as well as the structure of yellow fever virus NS3-protease. We will also present the ensuing collaborative efforts towards the identification on inhibitors and development of novel antiviral lead candidates. We will also report our current progresses in the structural and functional studies of flaviviral replication complex and initial structural work with chikungunya virus proteins. These collaborative projects are conducted within the interinstitutional Center for Research and Innovation in Biodiversity and Drug Discovery (CIBFar/CEPID/FAPESP).
Gonçalo Bernardes
University of Cambridge, UK
Instituto de Medicina Molecular, Lisbon, Portugal
After completing his D.Phil. degree in 2008 at the University of Oxford, U.K., he undertook postdoctoral work at the Max-Planck Institute of Colloids and Interfaces, Germany, and the ETH Zürich, Switzerland, and worked as a Group Leader at Alfama Lda in Portugal. He started his independent research career in 2013 at the University of Cambridge as a Royal Society University Research Fellow, and in 2018 he was appointed University Lecturer. His research group interests focus on the use of chemistry principles to tackle challenging biological problems for understanding and fight cancer.
MedChemComm Emerging Investigator Lectureship: Chemical Physiology of Antibody Conjugates and Natural Products
Our research uses chemistry principles to address questions of importance in life sciences and molecular medicine. This lecture will cover recent examples of emerging areas in our group in:
- methods developed for site-selective chemical modification of proteins at cysteine, disulfide and lysine and their use to build stable and functional protein conjugates for in vivo applications [1–4]
- bioorthogonal cleavage reactions for targeted drug activation in cells [5,6]
- by identifying on- and off-targets for anti-cancer entities using our own machine intelligence platform, unveiling the underlying molecular mechanisms of target recognition and linking drug target binding to modulation of disease, we explore the use of natural products as selective cancer modulators [7]
- Bernardim B; Cal PMSD; Matos MJ; Oliveira BL; Martínez-Sáez N; Albuquerque IS; Corzana F; Burtoloso ACB; Jiménez-Osés G; Bernardes GJL* Stoichiometric and Irreversible Cysteine-selective Protein Modification using Carbonylacrylic Reagents. Commun.2016, 7, 13128.
- Martínez-Saez N; Sun S; Oldrini D; Sormanni P; Boutureira O; Carboni F; Compañón I; Deery MJ; Vendruscolo M; Corzana F; Adamo R; Bernardes GJL* Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo. Angew. Chem. Int. Ed.2017, 47, 14963–14967.
- Freedy AM; Matos MJ; Omar Boutureira O; Corzana F; Guerreiro A; Somovilla VJ; Rodrigues T; Nicholls K; Xie B; Jiménez-Osés G; Brindle KM; Neves AA; Bernardes GJL* Chemoselective Installation of Amine Bonds on Proteins Through Aza-Michael Ligation. J. Am. Chem. Soc.2017,139, 18365–18375.
- Matos MJ; Oliveira BL; Martínez-Sáez N; Guerreiro A; Cal PMSD; Bertoldo J; Maneiro M; Perkins E; Howard J; Deery MJ; Chalker JM; Corzana F; Jiménez-Osés G; Bernardes GJL* Chemo and regioselective lysine modification on native proteins. J. Am. Chem. Soc.2018,140, 4004–4017.
- Stenton BJ; Oliveira BL; Matos MJ; Sinatra L; Bernardes GJL* A Thioether-directed Palladium-cleavable Linker for Targeted Bioorthogonal Drug Decaging. Chem. Sci.2018, 9, 4185–4189.
- Sun S; Oliveira BL; Jiménez-Osés G; Bernardes GJL* Radical-mediated thiol-ene strategy for photoactivation of thiol-containing drugs in cancer cells. Angew. Chem. Int. Ed.2018, DOI: 10.1002/anie.201811338.
- Rodrigues T; Werner M; Roth J; da Cruz EHG; Marques MC; Akkapeddi P; Lobo SA; Koeberle A; Corzana F; da Silva Júnior EN; Werz O; Bernardes GJL* Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor. Chem. Sci.2018, 9, 6885–7018.
Greg Basarab
Drug Discovery and Development Centre (H3D)
University of Cape Town, South Africa
Greg Basarab has an appointment as Principal Research Officer and Associate Director at the University of Cape Town (UCT) and the affiliated Drug Discovery and Development Centre (H3D). He leads research teams in Medicinal Chemistry, DMPK and Microbiology directed toward the eradication of resistant infectious diseases including malaria and tuberculosis. He contributes lectures in Pharmacology, Toxicology and Medicinal Chemistry at the UCT Medical School and is co-organizer of the Wellcome Genome Campus Advanced Campus course on Drug Discovery. Currently, he sits on scientific advisory boards of CARB-X (Combating Antibiotic Resistant Bacteria), the Global Antimicrobial Research & Development Partnership (GARDP) and the South Africa MRC (Medical Research Council). Previously, he was an Associate Director at AstraZeneca where he led multi-disciplinary teams for the design of novel mode-of-action antibacterials that delivered zoliflodacin, an anti-gonorrhea drug currently in Phase 3 human clinical trials and an MRSA agent (now discontinued) to Phase 1. He also contributed to a b-lactam/b-lactamase inhibitor combination progressing through Phase 2. Before that, he worked at DuPont leading projects in three departments: Central Research & Development, Biochemicals and Agricultural Products in the antifungal arena and in automated chemical synthesis. He received a B.S. in Chemistry from Penn State University and a Ph.D. in Chemistry from MIT.
Plasmodium Kinases – Novel Targets for Antimalarial Drug Discovery
The Drug Discovery and Development Centre (H3D) at the University of Cape Town and the Medicines for Malaria Venture have jointly discovered MMV048, a potent antimalarial oral agent that has progressed into Phase 2 clinical trials. The attributes of the clinical candidate include the lack of pre- existing resistance, a favourable safety profile and the possibility for a single dose cure, due, in part, to superior pharmacokinetics. Besides providing an anticipated valuable medicine for the devastating disease, the discovery work around MMV048 uncovered a novel target, namely Phosphatidylinositol 4-Kinase (PI4K), which more broadly asks the question: Which other Plasmodium kinases could be targeted for the discovery of next generation antimalarial agents? With this question, it is recognized that the pharmaceutical industry has had exceptional success in selectively targeting human kinases to develop a variety of life-saving medicines for oncology, cardiovascular and inflammatory diseases. Prompted by such work with human kinases, presented will be efforts at the University of Cape Town in partnership with others to further exploit PI4K and explore other Plasmodium kinases towards the discovery of new antimalarials.
Hatylas Zaneti de Azevedo
Research, Development & Innovation
Aché Laboratórios Farmacêuticos
Building a target and drug discovery environment in Brazil through research platform-based partnerships
In this presentation, I will show the recent efforts of Aché Laboratórios to enable radical innovation in Brazil by establishing strategic partnerships in research platforms of interest to the company. In particular, it will be presented the drug discovery collaborations in research areas such as natural products and small molecule cancer drugs.
Jadel Kratz
Drugs for Neglected Diseases initiative (DNDi), Latin America
PhD in Pharmacy at the Universidade Federal de Santa Catarina (UFSC), Brazil (2011). R&D Coordinator at Cristália Produtos Químicos e Farmacêuticos, Brazil (2014-15). International R&D experience at University of Innsbruck (Austria, 2012-13) and Uppsala University (Sweden, 2010). Involved in multiple preclinical projects focused on in silico and in vitro development of drug candidates. Managing collaborative Drug Discovery projects for Neglected Tropical Diseases. Strong backgroundin Medicinal Chemistry and International Collaborative Networks. Experience with Brazilian Pharma and academic R&D groups in Brazil, Sweden and Austria.
Novel collaborative approaches boosting R&D for neglected tropical diseases
Neglected tropical diseases (NTDs) are a diverse group of communicable diseases that prevail in tropical and subtropical conditions and affect more than one billion people. Chronic, highly debilitating and potentially lethal diseases, the NTDs not only have direct health impact in the patients, but also decrease earning ability and increase unemployment, thus generating a tremendous social and economic impact, perpetuating the poverty cycle in the affected regions. The pharmacotherapy available up to date for NTDs is largely unsatisfactory. Lack of efficacy, toxicity, long course treatments, emergence of resistant strains, and high cost are some of the associated problems. The identification of novel, effective, safe, and cheap drugs is urgently needed. At the same time, the efforts to discover and develop new drugs have been hampered by many challenges linked mostly to the partial understanding of the diseases. The lack of suitable assays to assess drug efficacy, a relatively little financial support, a fragmented research community, and the lack of appropriate tools convert the translation from preclinical findings into registered and accessible drugs into an immense challenge. The Drugs for Neglected Diseases initiative (DNDi) is a not for profit R&D organization guided byNTDs patients’ needs. Since 2003, it has been working hard to overtake the aforementioned hurdles and make new and affordable treatments available to all patients. Apart from its core drug discovery and development activities, DNDi harnesses and strengthens R&D capacity in disease endemic regions to generate a sustainable scientific environment around NTDs, and advocates for policy change towards widespread availability of treatments. A range of innovative and flexible collaborative models have been applied to tackle the challenges of developing safe, effective, and field adapted treatments for patients suffering from neglected diseases including sleeping sickness, leishmaniasis, Chagas disease, filarial infections, mycetoma, paediatric HIV infection, and hepatitis C virus (HCV) infection. This presentation will a provide a brief overview on DNDi’s organizational model and how it is boosting the R&D for neglected diseases worldwide.
José L. Medina Franco
Universidad Nacional Autónoma de México, México
Associated Editor of the journals RSC Advances and Molecular Diversity
Jose L. Medina-Franco holds a BSc in Chemistry (National Autonomous University of Mexico (UNAM), a MSc and Ph.D. degree (both from the UNAM). In 2005, Dr. Medina Franco joined the University of Arizona as a postdoctoral fellow and he was named Assistant Member at the Torrey Pines Institute for Molecular Studies in Florida. In 2013, he conducted research at the Mayo Clinic. In 2014 he joined UNAM as Principal Investigator and Full Time Research Professor. He has been named Fellow of the Royal Society of Chemistry (UK). Jose has published more than 185 peer-reviewed papers, 20 books chapters and issue one international patent. He has edited the books Epi-Informatics and Food Informatics. Jose serves as Associated Editor of the journals RSC Advances and Molecular Diversity. He currently leads the DIFACQUIM research group at UNAM. His research group has received several research grants funded by government institutions and pharmaceutical companies. Jose has supervised the research of 8 postdoctoral fellows, 6 PhD students, 5 Masters and 15 Undergraduate students. The research focus is on chemoinformatics and computer-aided drug design with applications on epigenetic targets, natural products, and peptides.
Epigenetic drug discovery: a focus on activity landscape modeling
Epigenetics is defined as the study of the chromosomal mechanisms that induce heritable changes in gene expression without modification of the DNA sequence and that lead to a stable phenotype. These epigenetic regulations can be mediated by the methylation of DNA or by post-translational modifications of the histones and affect the structure of the chromatin. The augmented interest in epigenetic drug discovery has promoted the development and maintenance of large information on structure–epigenetic activity relationships for several epigenetic targets. In turn, such large databases are rich sources of information to explore their structure–activity relationships (SARs) and structure– multiple activity relationships (SmART). In this talk, we report the findings of a large-scale analysis of the SAR and SmART of epigenetic targets using the concept of activity landscape modeling. Quantitative analysis and a novel visual representation of the epigenetic activity landscape enabled the rapid identification of regions of targets with continuous and discontinuous SAR. This information led to the identification of epigenetic targets for which it is anticipated an easier or a more difficult drug-discovery program using conventional hit-to-lead approaches. The insights of this work also enabled the identification of specific structural changes associated with a large shift in biological activity.
Laurent E. Dardenne
National Laboratory for Scientific Computing – LNCC/MCTIC, Petrópolis – RJ – Brazil
Laurent Emmanuel Dardenne has a B.Sc. degree and an M.Sc. degree (1995) in Physics from Universidade de Brasília. Obtained a Ph.D. in Biophysics from Universidade Federal do Rio de Janeiro in 2000. He joined the Brazilian National Laboratory for Scientific Computing (LNCC) in 2002 and is the leader of the Biological Molecular Modeling Group at LNCC. He is an expert in the field of computational chemistry, and his main lines of research are related with the development of new algorithms, methodologies, software and web servers for structure-based drug design and protein structure prediction. He also works in the field of drug design in collaboration with medicinal chemistry research groups.
Protein-Ligand Docking: Pose and Binding Affinity Prediction
Protein-ligand docking is an important tool for structure-based rational drug design studies. This method aims to predict the experimental binding mode and affinity of a small molecule within the binding site of the protein target of interest. The DockThor program, developed by our group GMMSB/LNCC, uses a grid-based methodology and was implemented to deal with highly flexible ligands using a multiple-solution steady-state genetic algorithm. The pose prediction scoring function is based on the MMFF94S classical force field, and, recently, our group developed linear and non-linear affinity scoring functions (general and target-specific). In this talk, we will show some recent methodological developments associated with the DockThor program and comparative analyses for pose and affinity predictions with other state-of-the-art docking programs. We will also discuss some DockThor developments under progress. The DockThor-VS portal (freely available for the scientific community at www.dockthor.lncc.br) utilizes the computational facilities provided by the SINAPAD Brazilian High-performance Platform and the petaflop supercomputer Santos Dumont.
Lídia Moreira Lima
Federal University of Rio de Janeiro, Brazil
Lídia Moreira Lima was born in Rio de Janeiro/Brazil in 1972 and graduated from the Federal University of Rio de Janeiro in 1995 as Pharmacist. She got MSc degree in 1997 from Chemistry Institute of Federal University of Rio de Janeiro (UFRJ). In 2001, she got the “Doctor of Chemical Science” degree in the subject of Medicinal Chemistry from Chemistry Institute of UFRJ. From 2002 to 2013 she was Associate Professor at the Faculty of Pharmacy in the Federal University of Rio de Janeiro. She conducted post-doctoral research at the Department of Pharmaceutical Chemistry at the University of Navarra, Spain (2004-2005). She is an Associate Professor in the Biomedical Institute of Sciences from Federal University of Rio de Janeiro. Her main scientific interests involve the molecular design, synthesis, metabolism study and lead-optimization of new drug candidates for cancer, diabetes and neglected diseases.
Discovery of new small molecules designed as antitumor candidates
Cancer is a serious public health problem worldwide, victimizing millions of people annually. Targeted cancer therapies, which include mAbs and small molecule inhibitors, have significantly changed the treatment of cancer over the past 15 years. They are designed to interfere with specific molecules necessary for tumor growth and progression, aiming to fight cancer cells with more precision and potentially fewer side effects. Drugs for targeted therapies are primarily tyrosine kinase inhibitors that have noticeably changed outcomes for some cancer diseases. In this summary, we will present the efforts of our research group aimed at the search of new antitumor candidates, acting through the inhibition of epidermal growth factor receptor (EGFR) and phosphoinositide 3-kinases. The molecular design, docking studies, synthesis, drug-likeness profile and cytotoxic effect of new EGFR and PI3K inhibitors will be presented and discussed.
Luis Octavio Regasini
São Paulo State University(UNESP), Brazil
Luis Octavio Regasini was born in Andradina/Brazil in 1979 and has graduated at the São Paulo State University (Unesp) in Araraquara Campus as Pharmacist. He has obtained his PhD in Chemistry at the Unesp (Araraquara Campus), in 2008. In 2013, he started his independent career as Professor of Organic and Medicinal Chemistry at the Unesp (São José do Rio Preto Campus). He was visiting professor of Groningen University – The Netherlands (Top 100 Global Universities), in 2015. His recent awards and distinctions include Hans Viertler Award for Young Scientist – Brazilian Chemical Society (2019) and Member of the São Paulo State Science Academy (2019). His research interests are focused on the discovery anti-infective and antineoplastic electrophilic compounds. He has 108 publications related to Medicinal Chemistry and Natural Products Chemistry.
Potential Antineoplastic and Anti-Infective of α,β-Unsaturated Ketones: A contribution of the Electrophilic Compounds
The concepts of electrophilicity and nucleophilicity constitute pivotal principles of organic chemistry which are paramount relevance to our understanding of chemical reactivity. Electrophilic natural products (NP) form a structurally diverse set of compounds which are biosynthesized by life kingdoms. Potent examples exist in all major classes of natural products, which can be separated in three main classes: Michael acceptor systems, ring-strained scaffolds and others (such as sulfur- and cyano-compounds). They convey a wide variety of bioactivities, mainly antineoplastic and anti-infective. Also, there are several examples of drugs with the mechanism of action based on their electrophilicity, such as acetylsalicylic acid, β-lactams, HCV-protease inhibitors (telaprevir and boceprevir), orlistat, clopidogrel, fosfomicin, esomeprazole and EGRF inhibitors (afatinib). In this lecture, I am presenting the chemico-biological experience of Antibiotics and Chemotherapeutics Laboratory in the investigation of bioactive α,β-unsaturated ketones, which belong to the chalcone, cinnamaldehyde-like and curcumin-like classes. In the last six years, about 400 α,β-unsaturated ketones were synthesized and evaluated against bacteria (ESKAPE group and Mycobacterium tuberculosis), fungi (Candida and dermatophytes), as well as human and canine tumorigenic cancer cells. For the bioactive α,β-unsaturated ketones, their mechanism of action was elucidated, suggesting as their molecular targets: p53 protein (antineoplastic compounds), FtsZ protein (antibacterial compounds) and ergosterol pathway biosynthesis (antifungal compounds).
Marcio V Bertacine Dias
University of São Paulo, Brazil
Dr. Marcio Vinicus Bertacine Dias is graduated in Biological Science by São Paulo State University (UNESP), campus São José doRio Preto (IBILCE), 2004. He has a Ph.D.in Molecular Biophysics by the same Institute in 2007. He worked as a Research Associate at the Universityof Cambridge for more than 4 years on the supervision of Sir Tom Blundell and Prof. Chris Abell between 2007 and 2011. He was a Young Research Fellow of FAPESP at National Laboratory of Bioscience between 2012 and 2014 and currently, he works as an AssociateProfessor at Department of Microbiology on the Institute of Biomedical Science of University of São Paulo. He has experience in structural biology (crystallography), isothermal calorimetry titration and other biophysics techniques and fragment-baseddrug discovery. Recently he was appointed for the position of Assistant Professor in Biomolecular Structure at Department of Chemistry, University of Warwick, UK. He currently works with fragment-based drug discovery applied to target enzymes from Mycobacterium tuberculosis, and enzymology and structural biology of natural product biosynthesis, including aminoglycosides and polyether ionophores applied to synthetic biology.
Identifying Novel Inhibitor Scaffolds for the Mycobacterium tuberculosis Dihydrofolate Reductase Using a Fragment-Based Drug Discovery Approach
Dihydrofolate reductase (DHFR) is an important target for several antibacterial and anticancer drugs and, although this protein has been extensively studied in several organisms, including human, bacteria, andprotozoa, some questions still remain to be addressed. Recently, our research group and others obtained new insights about the mechanistic of this enzyme during the catalysis, revealing two conformation states for some DHFRs. Based on that, differentorganisms might have distinct conformational changes during the binding of the substrate and cofactor that could implicate into distinct modes of binding and affinity for the antifolate drugs. Interestingly, antifolate drugs, such as trimethoprim and pyrimethamine, are not used in the treatment of tuberculosis and these compounds seemto have low affinity for MtDHFR. Using an integrative strategy of Fragment-Based Drug Discovery (FBDD), we have identified novel molecules that have completely new scaffolds among the HDFR inhibitors. From an initialscreening of about 1,200 molecules, we have extensively validated about 20 molecules through ITC and NMR and using crystallography we have obtained the structure of MtDHFRin complex with 8 of them. One of the unusual fragments binds in a specific site of MtDHFR with an affinityof 600 µM and using fragment growing, we have reached compounds with a 16 µMaffinity with a completely distinct structure and binding mode in comparisonto other antifolates. Although these compounds have not yet tested against M. tuberculosis, this strategy showed tobe promising in identifying new DHFR inhibitors that might have selectivity against this bacterial enzyme and open perspective in the development of new drugs against tuberculosis.
Maria Cristina Nonato
School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo
Drª Maria Cristina Nonato have over 25 years of experience in the field of Structural Biology, integrating biophysics chemistry and biology with the goal of advancing human health, in particular in the fields of neglected and rare diseases.
Fragment screening against human prion protein
Prion diseases are progressive neurodegenerative disorders that affect both humans and animals. They are associated with the conformational conversion of the cellular prion protein PrP into PrPSc, a self-replicating isoform (prion) that accumulates in the central nervous system of affected individuals. The mechanism underlying the PrP-to-PrPSc conversion and subsequent aggregation remains to be elucidated. At present, no specific therapeutic and prophylactic interventions are available for prion diseases. Compounds that stabilize the PrP health conformation represent a promising strategy to inhibit prion propagation. Due to lack of canonically druggable cavities in PrP, fragment screening emerges as unique technique to advance our knowledge of how and where to target PrP. This approach entails screening libraries of very small molecules that follow the “rule of three” criteria and an efficient search of diverse chemical space. In our work, we combine the state-of-art technology in X-crystallography fragment screening with biophysical and biochemical tools, to identify and validate compounds that are able to bind and stabilize the cellular form of PrP found in healthy organisms. In this presentation, we will present our most recent findings in the search for PrP binders and will highlight the relevance of this approach in the process of drug discovery. This project has been performed in collaboration with Broad Institute at MIT and Harvard and Diamond Synchrotron source in UK.
Mario Cardozo
Nurix, Inc., USA
Dr. Cardozo obtained a PharmD and Ms. Degree in Organic Chemistry from the National University of Cordoba, Argentina. He completed a PhD in Pharmacy from the University of Buenos Aires, Argentina. Subsequently Dr. Cardozo was awarded an NIH Fogerty International Fellowship to carry on post-doctoral research work in Computer-Aided Drug Design (CADD) at the University of Illinois at Chicago, under the advice of Prof. Tony Hopfinger. Dr. Cardozo has more than twenty-five years of expertise, in the pharmaceutical industry, applying state-of-the-art computational chemistry methodologies to guide drug discovery efforts in a wide range of therapeutic targets and modalities. His industrial positions include; head of computational chemistry at Boehringer Ingelheim Pharm., Tularik Inc, Amgen Inc, M.D. Anderson (IACS), and Nurix Therapeutics. Dr. Cardozo has a strong experience building and directing world class computational chemistry groups. His focus has been on integrating CADD tools and rationales to project teams, and to enable full advantage of the technology. He has worked in many therapeutic targets including GPCR, kinases, nuclear receptors, and other proteins dysregulated in various disease pathways. In recent years, he has acquired strong experience on oncology and immuno-oncology targets that led to the discovery of several clinical candidates, some of them are currently in clinical trials. Most recent work includes the regulation of protein homeostasis by controlling protein degradation through the Ubiquitin Proteasome System. He had key roles in designing E3 ligase modulators and bifunctional degrader molecules (PROTACs) to control dysregulated oncogenic proteins and target neo-substrate for proteasome degradation. In addition, Dr. Cardozo has expert knowledge of in-silico ADMET modeling, including AI and ML approaches. He also has performed and directed research to study protein structure and function, including molecular dynamics simulations, adaptive sampling as well as other protein modeling and design approaches. He has demonstrated the ability to manage, and coach, scientists in applying, as well as developing computational chemistry technologies to enable a more efficient drug discovery process. Dr. Cardozo has a strong track record on the discovery of potential novel therapeutics, as demonstrated in several relevant invention patents and more than 50 scientific publications.
Impact of Computational Chemistry on Challenging Drug Discovery Projects: Structure-Based Design of potent Protein-Protein Interaction Inhibitors and Modulators
This presentation will highlight the use of Structure-Based Drug Design in advancing initial HTS hits to LI and LO stages. The integration of CADD tools into Medicinal Chemistry teams will also be discussed and exemplified with two case studies. These examples will touch the challenge to bring two proteins together with a so-called “molecular glue” to repair the affinity loss of oncogenic mutated proteins to a key E3 ligase, and to increase substrate degradation. The second example will highlight the integration of computational; Chemistry, Biophysics and Medicinal Chemistry teams and tools to discover an exquisitely potent inhibitor of a key Protein-Protein Interaction, aimed to enhance apoptosis of cancer cell.
Mônica T. Pupo
University of Sao Paulo, Brazil
Mônica T. Pupo graduated in Pharmacy in 1990 from University of São Paulo (USP), Ribeirão Preto campus, and then earned her PhD in Chemistry from Federal University of São Carlos in 1997. She was a postdoctoral researcher at Physics Institute of São Carlos (IFSC), USP, for one year and then she joined the School of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), USP, in 1998 as assistant professor. She was appointed as associated professor in 2009 and full professor in 2019. She was a visiting scholar at Jon Clardy group, Harvard Medical School, Boston, USA, from 2006 to 2007, and is currently CNPq Research Fellow level 1B. She coordinates the Laboratory of Microbial Chemistry at FCFRP-USP. Her research interests include the chemistry, biology and ecology of natural products from microbial symbionts in interspecies interactions, and the rational discovery pharmacologically active natural products.
Chemical warfare in Nature inspires the discovery of antimicrobials
New technologies and new habitats have re-emerged microorganisms as prolific sources for prospecting new chemical scaffolds with pharmacological applications. Our research program aligns chemical ecology and natural products discovery by studying chemical defenses provided by bacterial symbionts to host insects. Ants in the Attini tribe (leaf-cutter ants) collect plant material in the environment to feed a fungus they farm in their colonies for nutritional purposes. A specialized fungal pathogen (genus Escovopsis) can suppress the ant colony by growing over the fungal food source. Ants cope with this fungal threat using physical methods of spores’ removal and also the symbiotic association with actinobacteria in their exoskeleton, which produce selective antifungal compounds active against the pathogen but not against the food source. We have systematically studied the chemical defenses produced by Attini-associated actinobacteria collected in different Brazilian biomes and also evaluated the natural products against human fungal, bacterial and protozoan pathogens. In this presentation, I will discuss examples of antileishmanial and antifungal compounds, highlighting the potential of natural products involved in complex natural microbial interspecies interactions to guide the discovery of new hits.
Nelilma C. Romeiro
Federal University of Rio de Janeiro, Macaé, Brazil
Nelilma Correia Romeiro is a Pharmacist, got her degree from the Federal University of Rio de Janeiro (1996), a Master in Science (Organic Chemistry) from the Federal University of Rio de Janeiro (1998), under the supervision of Professors Ricardo Bicca de Alencastro (IQ-UFRJ) and Eliezer Barreiro (FF- UFRJ) and holds a PhD in Science (Organic Chemistry) by the Federal University of Rio de Janeiro (2002), under the supervision of Professors Ricardo Bicca de Alencastro and Magaly G. Albuquerque. She has also done a sandwich PhD at the University of Illinois at Chicago (UIC) under the guidance of Professor Anton J. Hopfinger, worked in LASSSBio-UFRJ under the supervision of Professor Eliezer Barreiro and completed a postdoc in Cambridge-UK, under the guidance of Professors Robert Glen and Andreas Bender. Currently, she is an Associate Professor I at UFRJ / Macaé, and is also a Researcher, CNPq-Level 2, experienced in the field of Medicinal Chemistry, with emphasis on Chemogenomics and several tools in Molecular Modeling, aiming at discovering new drug candidates.
FEFF-QSAR-3D
Nick Furnham
London School of Hygiene & Tropical Medicine, UK
Dr.Nicholas has expertise in computatioal biology, machine learning / AI, genomics and structural biology. He joined the School as an independent investigator supported by a MRC Strategic Skill Fellowship in Methodology Research. Prior to this he was a staff scientist / post-doctoral research in the group of Prof. Dame Janet Thornton at the European Bioinformatics Institute (an outstation of the European Molecular Biology Laboratory). He completed his PhD under the supervision of Prof. Sir Tom Blundell in the Biochemistry Department at Cambridge University after a MSc. in Bioinformatics at Exeter University. His original undergraduate training in Biological Science, where he specialised in parasitology, was at King’s College London.
Fragment-based discovery of Schistosoma mansoni Thioredoxin Glutathione Reductase (SmTGR) inhibitors: Second generation of structurally optimized leads identified by X-ray crystallography
The development of novel therapeutics is urgently required for diseases where existing treatments are failing due to the emergence of resistance. This is particularly pertinent for parasitic infections of the tropics and sub-tropics, referred to collectively as neglected tropical diseases, where the commercial incentives to develop new drugs are weak. One such disease is schistosomiasis, a highly prevalent acute and chronic condition caused by a parasitic helminth infection, with three species of the genus Schistosoma infecting humans. Currently, a single 40-year old drug, praziquantel, is available to treat all infective species, but its use in mass drug administration is leading to signs of drug-resistance emerging. To meet the challenge of developing new therapeutics against this disease, we have been developing and applying a combination of computational, phenotypic and target based approaches. This has included:
- the development of a computational drug repurposing pipeline supported by phenotypic screening;
- detailed reconstruction of all human infective Schistosoma kinomes;
- the use of structure-guided fragment-based drug discovery methods;
to identify new targets and new inhibitors that can provide novel leads in the development of new anti-schistosomal interventions. Our work has been driven by a need to develop a therapeutic that is effective not only across the three main infective Schistosoma species but against all three infective life stages that occur in humans. The work presented here will focused in particular on our application of fragment-based drug discovery techniques and the challenges of elaborating these fragments to produce high affinity binding drug like compounds.
Osvaldo Andrade Santos Filho
Professor at the Walter Mors Natural Products Research Institute (IPPN) of UFR
Osvaldo Andrade Santos Filho graduated in Industrial Chemistry in 1992 from Nuno Lisboa United Colleges; Specialist in Economic Engineering and Industrial Administration from Federal University of Rio de Janeiro (UFRJ) in 1995; M.Sc and Ph.D. in Chemistry from Military Institute of Engineering (IME) in 2000. He was a postdoctoral researcher at the College of Pharmacy of the University of Illinois at Chicago, United States of America, and at the Department of Organic Chemistry of the UFRJ. He was a research associate at the Faculty of Medicine of the University of British Columbia, Canada. He was a researcher at the Fundação Oswaldo Cruz (Fiocruz). Currently, he is a professor at the Walter Mors Natural Products Research Institute (IPPN) of UFRJ. He has experience in Physical Chemistry, focusing on Molecular Modeling applied to Medicinal Chemistry and Structural Biology, acting on the following subjects: protein modeling, molecular docking, molecular dynamics simulation, QSAR modeling, rational molecular design.
Structure-Based QSAR Analysis of a Set of 4-Hydroxy-5,6-dihydropyrones as Inhibitors of HIV-1 Protease: An Application of the Receptor-Dependent (RD) 4D-QSAR
Receptor-dependent (RD) 4D-QSAR models were constructed for a set of 4-hydroxy-5,6-dihydropyrone analogue HIV-1 protease inhibitors. The receptor model used in this QSAR analysis was a HIV-1 protease (PDB ID 1d4s) crystal structure. The optimized RD 4D-QSAR models were not only statistically significant but also possess reasonable predictivity based on test set predictions. The proposed “active” conformations of the docked analogues in the active site of the enzyme are consistent in overall molecular shape with those suggested from crystallographic studies. Moreover, the RD 4D-QSAR models also “capture” the existence of specific induced-fit interactions between the enzyme active site and each specific inhibitor. Hydrophobic interactions, steric shape requirements, and hydrogen bonding of the 4-hydroxy-5,6-dihydropyrone analogues with the HIV-1 protease binding site model dominate the RD 4D-QSAR models in a manner again consistent with experimental conclusions. Some possible hypotheses for the development of new lead HIV-1 protease inhibitors can be inferred from the proposed RD 4D-QSAR models.
I am an innovative and successful medicinal chemist with diverse industrial and academic experience, a history of clinical candidate delivery and a strong background in synthetic organic, medicinal chemistry and chemical biology. In my industrial career at Pfizer and Amgen, I delivered advanced compounds in projects for most major disease targets: kinase inhibitors, GPCR agonists and antagonists, metabolic enzymes, ion channels and chromatin modifiers while working in the urology, oncology, allergy, respiratory and pain therapeutic areas. As the Professor of Medicinal Chemistry in the University of Oxford’s Nuffield Dept of Medicine I have had an expanding role in the Alzheimer’s Research UK Oxford Drug Discovery Institute (ARUK-ODDI), Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC). I lead the chemistry teams dedicated to designing and synthesizing open-access small molecule probes, with a focus on novel proteins. My group designs and synthesizes chemical probes to enable target discovery in dementia, oncology and inflammatory disease and develops new chemoproteomic and biophysical assays to characterize epigenetic inhibitors. The probes discovered in my labs are used by hundreds of groups internationally to elucidate the mechanism of epigenetic regulation, one of the most exciting new areas of human biology.
Fragment-Based Discovery of Chemical Probes for New Targets
Chemical probes are potent and selective small molecule inhibitors that can be used in cellular assays to induce a phenotype. We are developing chemical probes to enable target discovery in disease relevant cellular models. Direct crystallographic screening of fragments in target proteins (XChem) provides structure enabled hits for rapid development into chemical probes. We will describe out latest efforts to develop chemical probes for novel protein families such as the Nudix hydrolases.
Round Table – Industrial Environment & Entrepreneurship
Per Sunnerhagen
University of Gothenburg, Sweden
Per Sunnerhagen is professor in molecular biology, Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden. His main scientific interests are post-transcriptional cellular responses to stress, and discovery of antimicrobial agents. His research relies to a large extent on genome-wide genetic technologies in yeast, as well as using small molecules to probe biological pathways, at the interphase between molecular biology and chemistry. A current focus is discovery of antimalarial molecules, in particular against Plasmodium vivax. In collaboration with structural biologists, medicinal chemists, and malariaexperts, molecules that are candidates for interaction with the target proteins are identified and evaluated in vitroand in vivo. In this context, the group is also investigating new genetic techniques for Plasmodium. He has coordinated of the research platform “Chemical biology” at UGOT, and currently he leads the research infrastructure “Large scale cell-based phenotypic screening” at UGOT, which aims to shortly become part of the national Swedish chemical biology research infrastructure.
New molecules against Plasmodium vivax using yeast surrogate genetics
Plasmodium vivaxinfections present particular challenges both for the clinician and the experimental scientist. While P. vivaxaccounts for more than half of all malaria infections outside Africa, it has received less attention than P. falciparum as acute symptoms and lethality of P. vivaxmalaria are considerably less severe. However, P. vivax typically causes life-long infections because of a dormant liver stage that is hard to target with existing drugs. It is also not possible to cultivate P. vivaxin vitro, making testing of drugs against this organism challenging. There is thus a need for indirect approaches that would allow us access P. vivax protein targets. We collaborate with research groups in Brazil and Cambodia in a multidisciplinary effort in this direction, involving bioinformaticians, structural biologists, medicinal chemists, molecular biologists and malaria experts. We use a yeast-based system where human or parasite proteins are expressed in separate yeast strains, making survival of the strains dependent on the heterologous protein [1]. This allows us to probe small molecules for selective growth inhibition of the strain expressing the P. vivax ortholog over that expressing the human one, indicating specific inhibition of the parasite protein. We select new target proteins with a bioinformatics approach, identifying genes that are conserved between Plasmodium species and other eukaryotes and hence likely to be essential, belonging to druggable protein classes, and also rely on transcriptomics data from P. vivax-infected patients to ensure that target proteins are indeed expressed. To identify molecules for testing, in silico docking against target proteins is used. Promising candidates are evaluated in the yeast expression system, and those showing selective inhibition of the parasite version of the target protein are tested in vitrofor activity against Plasmodium and cytotoxicity. Further testing in mouse models and against drug-resistant Plasmodiumstrains will be done for the best candidates. We are also investigating improved methods for DNA transformation and genetic engineering of Plasmodium, including gene knockout. If successful, those techniques will be important for drug target validation in the parasite.
- Bilsland E et al, Open Biol3:120158 (2013)
Peter Warner
Bill & Melinda Gates Foundation, USA.
Dr Warner joined the Bill and Melinda Gates Foundation (BMGF) in 2013 after a 28-year career in the Pharma industry. Trained as a medicinal chemist, he has worked across a broad range of therapy areas delivering drug candidates to the clinic. Immediately prior to joining the BMGF he led the AstraZeneca Neglected Diseases Research Unit in Bangalore. Within the BMGF he manages a portfolio of grants focused primarily on tuberculosis and drug Discovery for Neglected Diseases. He is the co-leader of the TB Drug Accelerator consortium.
Discovery of Drugs to treat Neglected Disease
Millions of people suffer and die from diseases that disproportionately affect the poor. These include malaria and tuberculosis as well as a long list of other more obscure tropical diseases such as onchocerciasis. The Bill & Melinda Gates foundation (BMGF) is driven by the belief that every life has equal value. Providing the tools to improve the health of the poorest is a critical aspect of our work and this includes the discovery and development of drugs which will have the most impact on the lives of the poor. Often pharmaceutical companies cannot easily justify the significant investments needed to discover and develop drugs for these diseases. This is where the BMGF can step in and help to build partnerships and provide funding to de-risk drug discovery and development projects. The BMGF works with Product Development Partners including Medicines for Malaria Venture, The TB Alliance and Drugs for Neglected Diseases Initiative to harness the best academic research and couple it with research institute and pharmaceutical company partners to generate new drugs. One example of a network led by the BMGF is the TB Drug Accelerator and this will be described in more detail as an example of what can be achieved when world leading disease knowledge and biology is coupled with excellence in drug discovery.
Rodolpho C. Braga
Co-founder and CTO, inSilicAll, Brazil
Co-founder and CTO at inSilicAll, a Drug Discovery startup. Participating in BiotechTown’s acceleration program, the first private center in Brazil dedicated exclusively to the development of companies, products and businesses in the areas of Biotechnology and Life Sciences. BiotechTown is providing R$150.000 investment, the expertise of a senior team, networking, global partners (office in Boston – USA) and customized methodology to develop our business. Worked almost two years as a senior data scientist, toxicology and drug discovery specialist at Altox Alternative Toxicology Inc. In this role, he was responsible for the design and implementation of artificial intelligence system for a variety of interesting and challenging projects, including the development of the In Silico Toxicology Platform – iS-Tox® (http://www.is-tox.com). Worked 9 months on the Lead Optimization Latin America project (LOLA) by Drugs for Neglected Diseases initiative (DNDi), as a computational chemistry scientist. Also, he was a Visiting Professor in Medicinal Chemistry at the University of Turin (UniTO) (2015 – 2016). He was awarded a CINF Scholarship for Scientific Excellence of the American Chemical Society (ACS – 2014).
Design of an Artificial Intelligence System for Drug Discovery
The drug discovery process consists of many phases, and it often takes decades to be finalized. Also, the probability of failure is very high at every stage, as during preclinical phases, which the failure rates are over 99%. Artificial intelligence systems hold the potential of accelerating the drug discovery process by decreasing the scientists-spending time on the design of the development candidate. Thus, we employ multiple machine learning models structuring the basis of a multiparameter artificial intelligence system able to conduct small-molecule target/proteome screening, and PBPK modeling to improve the novelty, quality, and efficiency of preclinical drug discovery.
Sharon Prince
Professor and the Head of the Division of Cell Biology at the University of Cape Town (UCT).
Sharon Prince is a Professor and the Head of the Division of Cell Biology at the University of Cape Town (UCT) in South Africa (SA) and is currently a FAPESP funded Visiting Professor at the University of São Paulo in Brazil. Her research focuses on the identification and characterisation of novel therapeutic interventions and drug targets for the treatment of breast cancer, melanoma and sarcomas. She is internationally recognized as a pioneer and authority on the role and regulation of the transcription factors TBX2 and TBX3 in cancer. Her research has highlighted the potential of these proteins as biomarkers for the detection of several cancers as well as targets in the development of effective cancer therapy. Her group also investigates the potential of organometallic compounds as novel anticancer drugs and repositioning anti-malarial and anti-psychotic drugs for anticancer activity. Sharon was elected a member of The Academy of Science of South Africa (ASSAf) in 2017 and in 2018, she was recognised by UCT as one of its leading women innovators, commending her excellence in innovative research and as a role model in science. She has been a Visiting Research Fellow at the University of Rennes and the University Côte d’Azur in France and in the Department of Genetic Engineering in the School of Bioengineering at the SRM University, Chennai in India. In 2019 and 2011 she was awarded an Oppenheimer Memorial Trust Fellowship and in 2010 the Harry Crossley Senior Clinical Fellowship. She was appointed the Director of a breast cancer consortium funded by the Department of Science and Technology and Cancer Research Initiative of SA in 2012 and in 2017, she was invited to participate in a National Cancer Research Strategy forum to address SA’s research priorities.
Identifying novel drugs for the treatment of rhabdomyosarcoma
Rhabdomyosarcoma (RMS) forms in skeletal muscle and is the most common soft tissue sarcoma in children and adolescents. Current treatment is associated with debilitating side effects and treatment outcomes for patients with metastatic disease are dismal. Other than a need for alternative and more effective therapies there is also a growing appreciation for the need to understand the molecular underpinnings of RMS with the aim of identifying, in part, novel targets to develop highly specific and effective treatments with negligible adverse effects. To this end, this study adopts a two-pronged approach to identy novel drugs for the treatment of the two major RMS subtypes viz alveolar (aRMS) and embryonal (eRMS) RMS. In the first approach, a novel binuclear palladacycle, AJ-5, was investigated for its anti-cancer activity and its mechanism(s) of action in RMS cells. We show that the binuclear palladacycle, AJ-5, exerts potent cytotoxicity in RMS cells with IC50 values of ≤ 0.2µM and a favourable selectivity index of > 2. Furthermore, we show that AJ-5 inhibited the ability of RMS cells to survive and migrate and that it induces apoptotic and necrotic cell death through a mechanism involving its ability to induce DNA damage. Pharmacokinetic studies in mice show that AJ-5 has a promising half-life and that its volume of distribution is high, its clearance low and its intraperitoneal absorption is good. Together these findings suggest that AJ-5 may be an effective chemotherapeutic with a desirable and novel mechanism of action for treating drug-resistant and advanced RMS.
The second approach of our study involves a target-based drug repurposing strategy where a library of commercially available drugs was screened to identify leads that were able to negatively regulate the highly homologous oncogenic TBX2 and TBX3. These T-box transcription factors have both been implicated as key drivers of RMS and they have been identified as novel therapeutic targets for the treatment of this sarcoma subtype. Indeed, TBX2 and TBX3 overexpression and knock-down cell culture and mouse models show that RMS cells are addicted to them for their cancer phenotype. However, targeting transcription factors is notoriously challenging because unlike enzymes they do not have catalytic activity and deep binding pockets to which small molecule inhibitors can be designed which is further exacerbated by the length of time and costs associated with de novo drug development. Therefore, the strategy adopted in this study is novel and circumvents these challenges by combining a drug repurposing with a targeted approach to TBX2/3. ‘Hits’ were identified by z-scores and HC StratoMineR analyses and amongst these, we have validated niclosamide, piroctone olamine and pyrvinium pamoate to be potent inhibitors of TBX2/3 and have shown that they display anti-cancer activity in in RMS. We provide evidence that these drugs have the potential to be repurposed for the treatment of RMS and other TBX2/3 driven cancers either as single agents or in combination with currently used chemotherapeutics.
Acknowledgements
This work was supported by grants from the SA Medical Research Council, the National Research Foundation (NRF), Cancer Association of South Africa (CANSA) and the University of Cape Town.
Sean Ekins
Founder and CEO of Collaborations Pharmaceuticals, Inc., USA
Sean graduated from the University of Aberdeen; receiving his M.Sc., Ph.D. in Clinical Pharmacology and D.Sc. in Science. He then went to the USA and was a postdoctoral fellow at Lilly Research Laboratories, before working as a senior scientist at Pfizer and then Eli Lilly. He went on to join startup companies as Associate Director of Computational Drug Discovery at Concurrent Pharmaceuticals Inc. (now Allergan) and Vice President of Computational Biology at GeneGo (now Thomson Reuters). Sean was CSO of Collaborative Drug Discovery, inc and co-founder and CEO at Phoenix Nest Inc.He is now founder and CEO of Collaborations Pharmaceuticals, Inc.which is focused on using machine learning approaches for rare and neglected disease drug discovery. He is also the on the SAB of the Pitt Hopkins Research Foundationand Adjunct Professor at 3 US universities. Since 2005 he has been awarded 20 NIH and DOD grants (STTR/SBIR grants, R21, UH2 and R01 as well as performs as a consultant on many others. He has authored or co-authored >300 peer reviewed papers, book chapters, and edited 5 books. For over 23 years he has been at the forefront of using commercial and in-house developed software in drug discovery research. He has a passion for finding new collaborators and developing new treatments for neglected and rare disease.
The Next Era of Pharmaceutical Research: From Bayesian Models to Deep Learning
Over the past decade our academic collaborations have encompassed applying machine learning to drug discovery for neglected diseases like Ebola, Chagas disease and tuberculosis. These have led to the discovery of drug-like molecules and repurposed drugs with in vivo activity identified using Bayesian Machine learning methods. In turn these efforts have resulted in grant funding from the NIH to further explore the molecules discovered. Additional recent academic collaborations include OpenZika, which has fostered a dynamic and fruitful interaction with our colleagues in Brazil and the support of IBM World Community Grid. These efforts promise to develop new molecules for neglected diseases. More, recently we have been exploring a wider array of machine learning approaches and this has coincided with the increase in use of deep neural networks (DNN). We have explored extensive curation of public datasets for neglected tropical diseases and compared many different algorithms and descriptors. We will summarize how newer methods like DNN performs versus other machine learning methods. We will also highlight our various collaborations and efforts to develop software such as Assay Central which allows the sharing of these models to enable drug discovery.
Sylvie Garneau-Tsodikova
University of Kentucky, USA
Associate Editor for MedChemComm
Sylvie Garneau-Tsodikova graduated in 1995 at the top of her class in chemistry and obtained her M.Sc. in 1997 from Université Laval (Québec, Canada) where she received numerous awards (Chemical Institute of Canada, National Sciences and Research Council of Canada “NSERC,” Fonds québécois de la recherche sur la nature et les technologies, Price Foundation, and Lucien Piché fellowship). She then joined the Ph.D. program in chemistry at the University of Alberta (Edmonton, Canada). During her graduate studies as an NSERC, Alberta Heritage Foundation for Medical Research and Izaak Walton Killam scholar, under the supervision of Professor John C. Vederas, she received rigorous training in chemistry and biochemistry. Her work in the Vederas’ group focused on the discovery and synthesis of new antimicrobial agents acting on bacterial cell walls. From Alberta, Dr. Garneau-Tsodikova moved to Harvard Medical School where she worked as a postdoctoral fellow in Professor Christopher T. Walsh’s laboratory. Through her studies on the formation and modification (halogenation) of mono- and dipyrroles in a variety of secondary metabolites, she obtained extensive training in mechanistic enzymology and strengthened her skills in biochemistry. From 2006-2013 she joined the University of Michigan as the John G. Searle Assistant Professor of Medicinal Chemistry in the College of Pharmacy and Research Assistant Professor in the Life Sciences Institute In April 2013 she joined the University of Kentucky as an Associate Professor of Pharmaceutical Sciences in the College of Pharmacy Using a multidisciplinary approach involving disciplines such as molecular biology, microbiology, biochemistry, as well as organic and medicinal chemistry, she is addressing several issues in synthetic biology and chemistry. Her research program has three main focuses: (i) the understanding of enzyme mechanisms involved in the biosynthesis of nonribosomal/polyketide antibiotics and anticancer agents as well as the development of new tools to generate and engineer novel nonribosomal peptides through combinatorial biosynthesis, (ii) the understanding and development of new molecules to combat bacterial resistance with a special focus on tuberculosis, and (iii) the development of multi-functional molecules for neurodegenerative disorders such as Alzheimer’s disease.
Towards understanding, engineering, and developing novel nonribosomal peptide enzymes
Nonribosomal peptides are natural products biosynthesized by multi-modular enzymatic assembly-lines comprised of domains performing various activities. Adenylating enzymes play a critical role in dictating the identity of building blocks to be incorporated in growing peptides during nonribosomal peptide biosynthesis. To increase the structural diversity of the products it generates, Nature has evolved unique interrupted adenylating enzymes capable of performing both adenylation and methylation reactions. We will present our efforts towards understanding the mechanism by which these unique enzymes function and our biochemical and structural work towards engineering novel interrupted enzymes with adenylating and methylating activities. We will also discuss the development of novel halogenating tools for natural product diversification.
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