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Research Team

The "Global Online Fight Against Malaria" project (or "GO FAM") is a research project run by Prof. Arthur J. Olson's laboratory in the Department of Integrative Structural and Computational Biology (DISCoBio) at The Scripps Research Institute in La Jolla, California.  The GO FAM data are currently being analyzed, tested, and extended in Associate Professor Joel S. Freundlich's lab in the Center for Emerging & Re-emerging Pathogens, Division of Infectious Diseases, Department of Medicine at Rutgers University-New Jersey Medical School.

The Scripps Research Institute, La Jolla, CA, U.S.A.

Prof. Arthur J. Olson is the GO FAM project leader.
Prof. Olson is a Professor of Integrative Structural and Computational Biology and Director of the Molecular Graphics Laboratory at The Scripps Research Institute. Professor Olson leads a large, multi-lab "program project" funded by the National Institutes of Health to develop new approaches to discover novel AIDS therapeutics based upon our ever-increasing knowledge of the structural biology of HIV. Now we're applying the tricks, tools, and strategies we've developed against HIV to advance the fight against multi-drug-resistant superbugs of malaria, as well.


Alex L. Perryman, Ph.D. was a member of Prof. Olson's laboratory at TSRI from August 1st, 2007, until October of 2013,  and he managed and performed the day-to-day operations for both the FightAIDS@Home project and the GO Fight Against Malaria project. The GO FAM project was designed and created by Dr. Perryman. See the blog he and Ari Fishkind wrote for Citizen IBM for more details. He has been studying structure-function relationships in proteins since 1996 (the summer before his freshman year started), when he worked in Prof. Cleo Samudzi's X-ray crystallography lab at the University of Missouri-Columbia (MU).  In 1998, Alex began applying molecular modeling techniques to advance cancer research when he was an undergraduate Beckman Scholar in Prof. Tom P. Quinn's lab at MU (also called Mizzou). As a biochemistry major at MU, Alex was both a National Merit Scholar and a Barry Goldwater Scholar (bestowed by the U.S. Congress to the top scholars in both math and science).  He has been performing computer-aided, structure-based drug design research against HIV since joining Prof. Andy McCammon's laboratory at UCSD in 2000, as a Howard Hughes Medical Institute (HHMI) predoctoral fellow. Alex received a Ph.D. in 2005 from the Biomedical Sciences program at the University of California, San Diego, in the Pharmacology Department. Alex is a molecular modeling guru and is an expert at using information about protein structures to guide the fight against disease. Dr. Perryman is now a member of Professor Joel S. Freundlich's lab at Rutgers University-NJ Medical School, in the Center for Emerging & Re-emerging Pathogens.  His research is focused on learning how to defeat multi-drug-resistant mutant "super bugs" of infectious diseases and on designing and evaluating potential new drugs that can help reduce human suffering. Alex L. Perryman's LinkedIn profile can be found by clicking here.

Stefano Forli, Ph.D., joined Prof. Olson's laboratory at TSRI on March 2008. He received his Ph.D in 2006 in Pharmaceutical Sciences at the Universita' degli Studi di Siena, Italy, after an industrial fellowship in SienaBiotech. His main expertise is in docking, high throughput virtual screening and structure-activity relationships. The aims of his research are to exploit protein structural information to identify novel, potentially-active molecules and to overcome multi-drug resistance.


Sargis Dallakyan, Ph.D., is a Research Programmer III in Prof. Olson's lab. He is responsible for the hardware and software environment for the "Molecular Graphics Laboratory," and he is the Lead Developer on the Python Molecular Viewer (PMV), which we use during parts of the preparation and analysis of the experiments we perform on FightAIDS@Home and on GO Fight Against Malaria. Dr. Dallakyan received his Ph.D. from the Yerevan Physics Institute.


Ruth Huey, Ph.D., joined Prof. Olson's laboratory at TSRI in 1993 as part of the team responsible for developing AutoDock and AutoDockTools(ADT), its graphical-user-interface(GUI). She received her Ph.D in Biochemistry from Boston University in 1979 followed by postdoctoral research at UCSD in the laboratory of Dr. Jon Singer and at TSRI (1981-1987) in the laboratory of Dr. Tony Hugli. She devoted the years between 1987 and 1993 to her three children.


Michael Pique
is the Director of Graphics Development for Prof. Art Olson's lab at The Scripps Research Institute. Mike has been on the staff of The Scripps Research Institute since 1986. His chief activities are interactive 3-D visualization and molecular modeling. At TSRI, he has designed and produced a series of video sequences and images illustrating scientific concepts for both research and educational purposes. He is currently involved in software design for protein and small-molecule docking and visualization, analysis of hydrogen-deuterium-exchange mass spectrometry data, and creating tangible molecular models that serve as computer input and output devices.


Associate Professor of Medicinal Chemistry Subhash Sinha, The Scripps Research Institute, La Jolla, CA, U.S.A.



Technical Consultants and Collaborators:

Freundlich lab at Rutgers University-New Jersey Medical School:  the subset of GO FAM data against Mycobacterium tuberculosis is being analyzed by Dr. Alex L. Perryman and Professor Joel S. Freundlich, in collaboration with Dr. Sean Ekins (of Collaborations in Chemistry), tested by Xin Wang and Tom Stratton, and extended by Dr. Shao-Gang Li and Dr. Steve Paget.


Associate Professor and Associate Research Fellow Jung-Hsin Lin, School of Pharmacy, National Taiwan University, Taipei, Taiwan, and Division of Mechanics, Research Center for Applied Sciences, and Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan


Professor John H. Elder, The Scripps Research Institute, La Jolla, CA, U.S.A. Dr. Elder is a Molecular Biologist in the Department of Immunology and Microbial Science and has been studying retroviruses for the past 37 years. He is a long-time collaborator of Dr. Olson's in development of intervention strategies to thwart HIV infection and will lend his expertise in protein chemistry to the malaria project.


Ying-Chuan Lin, Ph.D., Staff Scientist in the Department of Microbial Science, in Prof. John Elder's lab at TSRI. Dr. Lin is a Molecular Virologist with expertise in the development and testing of anti-viral agents and enzyme purification and analysis. He will aid the malaria project in the cloning, expression, and biological assays of potential protein targets for development of drug treatments.


Associate Professor Bruce Torbett, The Scripps Research Institute, La Jolla, CA, U.S.A.


Gira Bhabha, Ph.D., University of California, San Francisco, San Francisco, CA, U.S.A.



InhibOx, Ltd., founded in 2001 by Professor Graham Richards, is a spin-out from the Chemistry Department of the University of Oxford. InhibOx develops and applies novel computer-aided drug design tools in ligand and structure-based design, and cheminformatics. In addition to providing technical advice, InhibOx is sharing the homology models that they developed of the subtilisin-like serine protease (subtilases = PfSUB1), which we will use as targets on GO FAM. The personnel at InhibOx involved in the GO FAM project are:

Paul Finn, Ph.D., Chief Scientific Officer
Garrett M. Morris, D. Phil, Research Manager
Simone Fulle, a Marie Curie post-doctoral Fellow (ITN)
Jean-Paul Ebejer, a Marie Curie Doctoral Training Fellow (ITN)

Note:  As of April 2013, Dr. Garrett M. Morris is now the "Head of Computational Chemistry" at Crysalin, Ltd., in Oxfordshire, UK.


The Blackman laboratory is integrated into the Division of Parasitology at the UK Medical Research Council's National Institute for Medical Research (NIMR), Mill Hill, London. The work of the group focuses on the molecular and cell biology of the human malaria parasite, with a particular interest in the mechanisms involved in red blood cell invasion and exit (egress). The Blackman group is also sharing the homology models that they developed of the subtilisin-like serine protease (subtilases = PfSUB1), which we will use as targets on GO FAM. In addition, the Blackman group will perform the biological assays that will help us test, refine, and extend our computational predictions against the subtilases. The individuals in the group involved in the GO FAM project are:

Michael J. Blackman, Ph.D., Programme Leader
Chrislaine Withers-Martinez, Ph.D., Senior Investigator Scientist
Maria Penzo, Marie Curie Doctoral Training Fellow (ITN)

 


Reem Al Olaby is a Ph.D. student (Yousif Jameel fellow) at the American University in Cairo, Egypt, under the supervision of Dr. Hassan Azzazy, Dr. Rod Balhorn, Dr. Brett Chromy (UC Davis Medical Center), and Dr. Shoshana Levy (Stanford University). Reem received her bachelor degree from the Faculty of Pharmacy at Ain Shams University, following that she received The Nadhmi Auchi Young Arab Leader Fellowship from The American University in Cairo, Egypt, to pursue her masters degree in Biotechnology, under the supervision of Dr. Hassan Azzazy and Dr. Rod Balhorn. During her masters degree program, she worked on a project she proposed--generating "smart drugs" against the hepatitis C virus. To advance this antiviral research, she started performing computational studies involving virtual screens, in collaboration with Prof. Art Olson's Molecular Graphics Laboratory at TSRI, and creating homology models of drug targets for which crystal structures are not yet available (such as hepatitis C virus's E2 protein, in collaboration with Dr. Adam Zemla at Lawrence Livermore National Laboratory). After receiving the Yousif Jameel Ph.D. fellowship at The American University in Cairo, Reem continued working on the hepatitis C project by performing the experimental validation studies (wet lab assays) using two different techniques (Surface Plamon Resonance and Dual Polarization Interferometry). She performed these experimental assays to determine whether the compounds she discovered in virtual screens actually bind to the target protein with high affinity or not. This phase was done in collaboration with Dr. Jost Vielmitter (California Institute of Technology) and Dr. Brett Chromy, and it led to the discovery of several novel ligands that can be incorporated into what are called "Selective High Affinity Ligands" (SHALs). In previous studies by Balhorn, et al., SHALs have displayed nano-molar to pico-molar affinity with the target proteins.  Reem will continue her Ph.D. work by testing the new SHALs in vitro and in vivo, in collaboration with Caltech and Dr. Shoshana Levy.

Throughout her postgraduate studies at AUC, Reem took part in "Biocamp Egypt," where she earned second place as the best presenter and was nominated to represent Egypt in The Global Biocamp that was held in Boston at the Novartis Institute for Biomedical Research in 2009.  Her team was distinguished as one of the three best teams in that global competition. She was hosted on the Egyptian National TV for her success in The Global Biocamp.  Reem also took part in The Nadhmi Auchi Hepatitis C Virus campaign that focused on raising awareness about how hepatitis C is transmitted and how we can prevent its prevalence.  Reem is currently a research intern in Dr. Ali Sultan's lab at Weill Cornell Medical College in Doha, Qatar (WCMC-Q), where she is working on another aspect of her Ph.D. project by performing research to develop "smart drugs" against malaria.



Pictured from left to right: Alex, Stefano, Art, Mike, Sargis (from Nov. 2011).