Ernest Eliel Workshop â US and Cuba Collaboration in Chemistry

Chapter 5

Downloaded by UNIV OF FLORIDA on December 29, 2017 | http://pubs.acs.org Publication Date (Web): November 2, 2017 | doi: 10.1021/bk-2017-1257.ch005

Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery W. L. Scott,*,1 J. G. Samaritoni,1 M. J. O’Donnell,1 A. B. Dounay,2 A. A. Fuller,3 P. S. Dave,1 J. M. Sanchez,1 D. G. Tiano,3 and D. G. Rivera4 1Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202-3274, United States 2Department of Chemistry and Biochemistry, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, Colorado 80903, United States 3Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States 4University of Havana, Zapata y G, 10400, La Habana, Cuba *E-mail: [email protected]

This chapter describes the “Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery” carried out at the University of Havana in October 2016. Through lectures and laboratories Cuban students were educated in chemistry and biology while they applied their understanding to addressing a serious humanitarian challenge – discovering drugs for neglected diseases. The one-week workshop was conducted by both Cuban hosts and professors and students from three US institutions – Indiana University Purdue University Indianapolis (IUPUI), Santa Clara University and Colorado College. The workshop lectures ranged from macroscopic overviews of the drug discovery process, both scientific and economic, to more detailed presentations of the skills and scientific understanding required to carry out discovery research effectively. The lab portion utilized one of IUPUI’s Distributed Drug Discovery (D3) synthetic procedures. It was solid-phase based and enabled

© 2017 American Chemical Society Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

students to make 22 compounds which were then submitted for antimicrobial testing. As student education was taking place the Cuban-US collaborative nature of the workshop led to deeper scientific and cross-cultural understanding. These connections are certain to bear fruit in the scientific and educational work we are planning.


Introduction It is both an honor and pleasure to provide a chapter for this book commemorating Ernest Eliel. Whether we know it or not, all synthetic and computational chemists have been affected by his life and work. One of us (WS) remembers this personally: “My Ph.D. advisor, Professor David A. Evans was immersed, at the beginning of his career at UCLA, in the physical organic chemistry milieu of Saul Winstein and Don Cram. Evans introduced me to Eliel’s “Stereochemistry of Carbon Compounds” and with Eliel’s compendium of stereochemical insight and Evans’ mentoring I became 3-dimensional in how I understood and predicted a molecule’s chemical and biological properties.” Professor Eliel continues to impact my life. His personal connection to the University of Havana and his passion for education was honored at a symposium I attended on US-Cuba collaboration at the 2015 ACS National Meeting in Boston, and it was there that I met Professor Daniel Garcia Rivera from the University of Havana. As we talked it was immediately clear that our shared expertise in solid-phase synthesis of biomimetic molecules with drug discovery potential, coupled with a passion for education, could be fertile ground for a US-Cuba collaboration. That meeting with Daniel gave rise to a successful application to the ACS for the Global Innovation Grant that supported our “Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery”. In the fall of 2016 we carried out the one-week workshop at the University of Havana. This chapter describes the workshop, the expanding collaborations it catalyzed, and the future it promises. We again think of Professor Eliel - his scientific accomplishments, passion for education, and Cuban connection - and believe his spirit is still guiding and encouraging us.

Foundation for Cuban Workshop: Distributed Drug Discovery (D3) At the core of the workshop is the Distributed Drug Discovery (D3) program created at IUPUI in 2003 (1–6). D3 seeks to educate students in chemistry and biology while they apply their learned skills and understanding to helping solve a serious humanitarian challenge – discovering drugs for neglected diseases, which we define broadly as diseases that lack the financial incentives supporting a traditional drug discovery process. The distributed power of D3 is possible when the large problem of drug discovery is broken into smaller challenges implemented at multiple schools across the world. Students are educated in 64 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

chemistry and biology while simultaneously enlisting their distributed and combined efforts in the larger drug discovery goal. Key challenges for D3 are: •

•


•

•

•

•

Making available simple, inexpensive, powerful and reproducible chemistry laboratory procedures and equipment that allows distribution of D3 problem-solving syntheses to schools with limited resources. Enumerating large virtual catalogs of molecules readily accessible by D3 procedures and finding computational experts to help select molecules to make for a given disease target. Enlisting biological testing resources that are relevant to neglected diseases, either student-run or freely available, and providing relevant biological activity data. Implementing and coordinating the neglected disease drug discovery research component, both laboratory and theoretical, in a motivational educational framework. Managing all the components: tracking molecules made physically and computationally, arranging for their biological screening, and recording, analyzing and sharing data. Building and nourishing international collaborations and understanding among schools, researchers, educators and students.

D3 has already made significant progress addressing these challenges. The particular disease target for this Cuban workshop was drug resistant microbes. In this context we sought to extend the scope of D3, learn more about its current strengths and limitations, and use this understanding to improve future workshops and the global coordination and implementation of D3. In the process we hoped to build scientific and personal connections between Cuban and US chemists.

Workshop Overview IUPUI has conducted workshops based on D3 at multiple sites in the US (7–9) as well as in Russia, Poland and Spain (10). These experiences prepared us for the Cuban workshop. Participants The “Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery” was conducted at the University of Havana the week of October 17-21, 2016 (11). US participants were Professors William Scott (WS) from Indiana University-Purdue University Indianapolis, Indiana (IUPUI); Amelia Fuller (AF) from Santa Clara University (Santa Clara, California); Amy Dounay (AD) from Colorado College (Colorado Springs, Colorado), and three undergraduates – Priya Dave (PD) and Juan Sanchez (JS) (both fluent in Spanish) from IUPUI, and Daniel Tiano (DT) from Santa Clara University. Cuban participants were host Professor Daniel Garcia 65 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Rivera (DR) and 27 University of Havana students: 17 undergraduates, 6 masters, 3 Ph.Ds. and one postdoc (Figure 1).

Figure 1. Cuba Workshop Participants. (see color insert) Back in Indianapolis Drs. Marty O’Donnell (MO) and Geno Samaritoni (GS) provided essential educational and practical resources as they helped coordinate the workshop from a distance. Daily Program Each day the workshop began at 9 AM and ended by 5 PM. Over the course of the week there were 11 lectures by US professors, an active learning session, 4 presentations by Cuban students, a joint US/Cuban poster session and laboratory work which took place during a 2½ to 3 hr period each of three afternoons. There was time set aside for US and Cuban colleagues to discuss topics of mutual interest and propose future collaborations. Our days were quite busy, however it was not all work. Each day we socialized during a 2-hour mid-day break, at dinner, and after hours (Figure 2). These times provided a welcome and balanced opportunity to build on the trust and comradery generated during our intense shared scientific work and to learn about each other’s personal lives and culture in an unselfconscious and relaxed manner.

Lecture Component of the Workshop The workshop lectures ranged from macroscopic overviews of the drug discovery process, both scientific and economic, to more detailed presentations of the skills and scientific understanding required to effectively carry out drug discovery research. At the macroscopic level we sought to give students a balanced view of the strengths and limitations of drug discovery through pharmaceutical research. This industry has given us life-saving drugs for bacterial infections, diabetes, cancer, 66 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


HIV/AIDS and many other serious diseases. At the same time, drug discovery research for neglected diseases has languished because profit-driven research is not supported by small or poor patient populations.

Figure 2. Lunch Between Lectures and Lab. (see color insert)

We proposed the D3 concept and program as a way to address this economic limitation by having students participate in drug discovery (in this case antimicrobial agents) as they learn the fundamental scientific disciplines behind the process. From the general science level down to specific and applied detail they learn the scientific principles and procedures that enable them, in the lab portion of the workshop week, to immediately and meaningfully participate in drug discovery for a humanitarian cause.

Lectures at a Macro Level Lecture 1. “Short Course in Drug Discovery” (WS) In the first lecture WS covered general aspects of the drug discovery process. He provided an historical understanding of how drugs are discovered from natural products (modified or unmodified, often based on observations from indigenous scientists) to more contemporary computationally-driven drug discovery (Figure 3). Drugs were discussed whose origins could be traced back to a farmer’s observation of hemorrhaging cows (Warfarin as an anticoagulant) or a blood pressure lowering peptide in snake venom (Captopril to treat hypertension). At the other extreme, the discovery process for life saving HIV protease inhibitors was linked to a more intensive “rational” and computationally-based drug discovery approach. 67 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 3. Lecture Presentation (see color insert)

Lecture 2. “Neglected Tropical Disease Research at Colorado College: Design and Synthesis of New Drugs for African Sleeping Sickness” (AD) In the second lecture AD, who worked as a medicinal chemist at Pfizer prior to joining the faculty at Colorado College, gave an informed perspective on the challenges and economic realities of commercial drug discovery. She did this in an introduction to her talk, explaining how the high cost of commercial drug discovery causes many tropical diseases to be neglected by the pharmaceutical industry. As a potential solution to this problem AD described how her research students at Colorado College are addressing, in their hands-on research and as part of their educational training, this need for drugs to treat African sleeping sickness.

Lecture 3. The Distributed Drug Discovery (D3) Program (WS) WS gave a general lecture on the Distributed Drug Discovery (D3) program, which is at the heart of both the educational and lab portion of this workshop. D3 educates student scientists in drug discovery, applied synthesis and biological evaluation while connecting them to critical humanitarian drug discovery needs. As they learn theory and practice they become part of a large, internationally distributed research collaboration for the discovery of drugs to treat neglected diseases. D3 currently teams students at the Medical University of Lublin (Poland) and four sites in the United States: Colorado College, Goshen College, Santa Clara University, and IUPUI. With this workshop students and professors at the University of Havana (Cuba) became part of this international network. WS discussed three essential requirements for a D3 laboratory: 1) Powerful, reproducible synthetic procedures to enable the synthesis of large numbers of potential drug molecules. 2) Simple, inexpensive equipment to carry them out. 3) Large D3 virtual catalogs of combinatorially enumerated molecules accessible by these student-run D3 procedures. 68 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

All the current D3 procedures are carried out by solid-phase combinatorial chemistry using fundamental reactions developed in solution (12, 13) and on solid-phase (3–6, 14–32). The solid-phase nature enables multi-step syntheses to be successfully carried out with simple equipment on a micromole scale. The student or student teams can then select target molecules from these catalogs and synthesize, using the D3 procedures and equipment, 6 unique molecules at a time. In this fashion students distributed globally can synthesize large numbers of new molecules for evaluation against neglected disease targets. WS discussed each of these requirements in more detail.


1. Powerful, Reproducible D3 Synthetic Procedures Nine D3 protocols are now in place (Scheme 1). D3 Labs 1 (4), 3 (5) and 9 (33) have been published.

Scheme 1. Nine D3 Protocols. 69 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

2. Simple, Inexpensive Equipment To Carry Out the Syntheses


Students execute all D3 procedures using the simple Bill-Board equipment (34) shown in Figure 4. This equipment facilitates carrying out six simultaneous, separate solid-phase reaction sequences in a combinatorial grid.

Figure 4. Bill-Board Equipment with Vessels, Drain Tray and Collection Rack. With the US-Cuba embargo still in place, it wasn’t simple to make sure the necessary equipment and reagents were in place for the start of the workshop. First we made sure it was legal to transport to Cuba the Bill-Boards which would be our essential synthesis equipment. Fortunately, recent modifications to the US Export Administration Regulations had a license exemption category for certain items supporting the Cuban people entitled “License Exception Support for the Cuban People (SCP)”. Our Bill-Board equipment, which was purchased from personal funds and donated to Professor Garcia Rivera for his students’ use, fell into that category. There were no readily identified commercial services to ship them. So we carefully documented the Bill-Boards’ purpose and source, packed them in our luggage, and took them with us as we traveled - Greyhound bus to Chicago, plane to Miami, charter to Havana. As for needed reagents, DR arranged for those not already available in Cuba to be shipped from Germany, where he was doing summer research.

3. Large D3 Virtual Catalogs From available reagents and any of the nine combinatorial solid-phase procedures listed in Scheme 1, large virtual catalogs can be enumerated. For D3 Lab 1 we constructed a 24,416 member virtual catalog of molecules realistically accessible by student synthesis. We are in the process of enumerating virtual D3 catalogs based on all the other procedures. These catalogs can serve as raw material for computational chemists to select molecules for students to make as potential drug candidates for neglected diseases. While the generic structures 1 and 9, from D3 Lab 1 and 9 respectively (Scheme 1), may appear quite uninteresting, compounds 1a and 1b (Figure 5) show they can be quite complex, and compounds 1c and 1d, 9a and 9b, confirm that molecules present in virtual catalogs can be reproducibly made by students using these procedures in the US, Poland, Russia and Spain (D3 Lab 1) (4) or at IUPUI and Santa Clara University (D3 Lab 9). 70 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 5. Representative Molecules, from D3 Labs 1 and 9, Replicated by Separate Students.

Lecture 4. “Synthesis and Study of Peptoids and Related Peptidomimetics” (AF) AF was D3’s first external collaborator. In this lecture she relayed to our Cuban colleagues her extensive experience in the peptoid field, convincing workshop participants that peptoids, N-substituted glycine oligomers, offer an exciting scaffold to adapt to D3 (35). Peptoids are commonly prepared on solid support, and readily accessible primary amines introduce variable functionality (36). AF highlighted this robust and efficient synthesis, along with applications of peptoids from her own lab and from the work of others. She detailed use of peptoids as mimics of bioactive peptides (37, 38) and as materials (39), and described how large libraries of peptoids have been prepared and subjected to high-throughput screening campaigns to identify novel ligands for varied target proteins (40). The lecture also detailed her own work investigating structural features of peptoids (41–43), and on new efforts, including those from her lab, to diversify the peptoid scaffold by making modifications to the oligoamide backbone (44–46). In addition to their many interesting applications, peptoids seemed of particular interest to this audience because of their relevance to the work of DR’s lab, whose targets, including N-alkylated peptides, bear some structural similarities. Lectures on More Detailed and Applied Work Lecture 5. “Implementation of the D3 Lab at Colorado College” (AD) AD’s presentation highlighted the successful incorporation of D3 Lab 2 into the “Organic 2” course at Colorado College. Additionally, AD described her investigations toward a number of new extensions to the D3 platform. For example, in an effort to incorporate more green chemistry principles into the D3 learning experience, she created a research project assignment for her advanced organic synthesis course for majors. This assignment required students to evaluate the D3 Lab 2 protocol using the 12 Principles of Green Chemistry (47, 48), propose a greener method, and then develop and optimize the new method in the 71 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

laboratory. She is currently following up on promising preliminary results from these student projects in order to identify greener methods for broader utilization across the D3 network.


Active Learning session: “Design of a Combinatorial Library of N-Acylated Amino Acids” (AD) AD has also developed a new pre-lab exercise at Colorado College to introduce students to the process of hypothesis-driven drug design. Following a talk describing this activity she conducted an active learning session with the student workshop participants. In this activity, students evaluated existing antimicrobial data for a series of amino acid derivatives accessible by D3 Lab 2 (which they were about to perform). Using the provided data, the students developed structure-activity relationship (SAR) hypotheses and proposed the next set of new analogs to be synthesized in the lab. Working first with a partner, and later with a larger assigned “medicinal chemistry team,” students had the opportunity to propose new design ideas, convince other team members of the ideas’ merits, and negotiate toward a final team proposal (Figure 6). The students were highly engaged in this exercise, which was intended to simulate a real-life medicinal chemistry team situation in which chemists must work together to prioritize ideas and agree upon a small set of high-priority synthetic targets.

Figure 6. Student Team Deciding which New Molecules to Make. (see color insert)

Lecture 6. “Combinatorial Synthesis of Aromatic Oligoamides” (AF) At an applied laboratory level AF described the implementation of her new D3 Lab 9 “peptoid” lab developed at Santa Clara University (Scheme 2). 72 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Scheme 2. New D3 Lab 9: "Peptoid Inspired" Lab Developed at Santa Clara U. Demonstrating that the D3 laboratory practices can be readily adapted to employ new chemistry, AF detailed the laboratory she teaches at Santa Clara University. In doing so, she also shared some photos and information about Santa Clara University and its students. This introduction prompted interest and amazement from the Cuban participants—in particular, they highlighted that they had never before seen a University affiliated with a church, indeed with a campus centered around it! But outside of the church and in this lab, AF’s students prepare combinatorial arrays of aromatic oligoamides. Students in the lab share with AF a long-term goal of identifying biological activities for this scaffold, which is structurally similar to other bioactive molecules. AF described how students used the Bill-Board apparatus to carry out the D3 Lab 9 six-step synthetic sequence and detailed synthetic results from a recent iteration of the lab course (33). As part of the D3 validation process 12 of the molecules her students made were independently replicated by a student at IUPUI using her published procedure. Lastly, she concluded her talk with short presentations on her ongoing efforts to develop new D3-compatible lab procedures to prepare additional molecules with medicinal potential.

Lecture 7. “D3 Pseudomonas aeruginosa (PA) Biofilm Project” (WS) In this lecture WS reported on the first D3 coupled chemistry/biology project (23, 31). It incorporated both D3 synthesis and D3 biological evaluation in student work that identified several potent inhibitors of P. aeruginosa (PA) growth. PA is a major cause of debilitating and deadly infections in patients with the orphan disease cystic fibrosis. Using simple, inexpensive, reproducible and powerful synthetic procedures, students made large numbers of unique unnatural amino acids in their second semester organic chemistry lab. In a subsequent microbiology lab course they tested these compounds against PA. Through this distributed process students identified several potent inhibitors of 73 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

PA. The active compounds are racemic, unnatural analogs of phenylalanine and its carboxyl derivatives. In follow-up studies individual enantiomers of three of the active racemic compounds were separated by chiral chromatography. Biological evaluation showed that in each case the biological activity resided almost exclusively in a single enantiomer. Literature precedent indicates these active compounds are functioning as antimetabolites, with implications for potential toxicity in humans. In subsequent undergraduate lab work we are further modifying the active molecules to seek derivatives that will have a greater therapeutic ratio.


Lectures Directly Related to Workshop Lab Lecture 8. “Solid-Phase Synthesis and Combinatorial Chemistry” (WS) Here WS discussed the chemistry and methodology that enables the molecules to be synthesized in the lab portion. Solid-phase synthesis (SPS) and combinatorial chemistry are crucial components of D3 laboratories because together they enable the efficient synthesis, on a small scale (typically 50 micromoles), of multiple compounds from a limited set of reagents - and with little loss of material. WS illustrated the essential SPS procedural steps and methodology with an example of the solid-phase synthesis of a tripeptide. This example also served to illustrate the power of combinatorial chemistry since 8,000 tripeptides could be made using SPS with access to 20 different amino acids at each position of the tripeptide (20 x 20 x 20 = 8,000). Students were instructed on how universal and fundamental the combinatorial synthetic process is in nature: millions of DNA sequences and proteins available from just 24 starting materials (“reagents”) - 4 nucleotides and 20 amino acids. They were now prepared to do in the lab their own combinatorial solid-phase organic syntheses based on the synthetic sequence of D3 Lab 2 (Scheme 3).

Scheme 3. D3 Lab 2: The Synthesis of N-Acylated Natural α-Amino Acids.

74 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Lecture 9. “D3 Lab 2: Reaction Mechanisms for Fmoc-Deprotection, N-Acylation and Resin Cleavage” (MO) Lecture 9 presented an opportunity to demonstrate distance learning aspects of D3. Electronically and in his physical absence, MO presented an audio-visual lecture (49) on the detailed mechanisms involved in each of the transformations conducted in the D3 Lab 2 synthetic procedure. Reaction mechanisms are an important aspect of the D3 program. They play a crucial role in explaining how known reactions proceed and rationalizing how unexpected by-products are formed. The D3 Lab 2 mechanisms tutorial illustrated each step of a reaction mechanism in dynamic “layered” audio-videos. It covered arrow-pushing, acid-based chemistry in terms of pKa’s and reaction equilibria, Le Chatelier’s Principle, reagent structures/acronyms, functional groups, nucleophiles/bases and electrophiles/acids, electronegativity, resonance, stereochemistry, racemization, etc. In his audio/visual lecture seven total ChemDraw schemes were discussed for the D3-2 laboratory (approximately 30 minutes total): 1) Synthesis Overview; 2) Arrow-Pushing and Acid-Base Chemistry; 3) Fmoc Deprotection; 4) and 5) N-Acylation; 6) and 7) Cleavage. Audio/video of the step-by-step progress of each reaction was presented. This and other audio-visual tutorials have been well received by students and instructors. They can be shown during lectures or, at IUPUI, as an out-ofclass assignment following a more general AV tutorial covering: Introduction to Research in the Lab; Choosing a Class of Targets; Background References; Amino Acids and Peptides as Drugs; Bill-Board Setup and Reaction Scheme; Individual ChemDraw Assignment (structures, SMILES, etc.) for each student team’s (13 students) Bill-Board; Reaction Inputs; Final Products (Fall 2016: 44 unique products unique products in 120 total reactions); Acknowledgements. Students can stop the tutorial at any point and replay it for a better understanding of the material. As demonstrated in this Cuba Workshop, with the link (49) given for this lecture, Audio-Visual Tutorials can be transported without the instructor.

Lecture 10. Compound Enumeration, Computational Analysis and “Teach-Discover-Treat” (WS) There was a brief lecture on compound enumeration of D3 virtual catalogs, computational analysis, and its application to searching these catalogs. After discussing the nature of some of the computational algorithms used in modeling work WS highlighted an ACS open-access computational project “Teach-Discover-Treat (TDT).” TDT fits well to a D3 model. In this ACS Computational Division initiative the computational community is challenged to develop computational models for neglected diseases. They should use freely available software tools and develop tutorials and models appropriate for educational purposes. The D3 community is closely following the progress of TDT, as linking it to D3 virtual catalogs could leverage its power by coupling 75 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

the educational and research capabilities of D3 synthesis to TDT computational analysis.

Lecture 11. D3 Collaboration with the Community for Open Antimicrobial Drug Discovery (CO-ADD) (WS)


This final lecture discussed the variety of ways by which molecules that students make can be evaluated for biological activity: 1) They can be tested by students as part of regular course work. For example, IUPUI’s microbiology students currently test molecules, made by IUPUI chemistry students, for their ability to inhibit the growth of Pseudomonas aeruginosa, a bacteria especially harmful to patients with cystic fibrosis (31). 2) They can be tested by academic collaborators (D3 collaborators are doing this in collaboration with microbiologists in Lublin, Poland). 3) Use commercial testing services (too expensive). 4) Use Open-Access resources a) Governmental (e.g. National Institutes of Health). b) Industrial (e.g. Lilly’s Open Innovation Drug Discovery program [“OIDD”]). c) Academic (e.g. Community for Open Antimicrobial Drug Discovery [“CO-ADD”]). Lecture 11 focused on that final test resource, CO-ADD, since it will be the testing site for compounds made by the Cuban students in their workshop lab. As stated on their website “CO-ADD is a not-for-profit initiative led by academics at The University of Queensland. Our goal is to screen compounds for antimicrobial activity for academic research groups for free. We aim to help researchers worldwide to find new, diverse compounds to combat drug-resistant infections.” CO-ADD screens compounds against the key “ESKAPE” pathogens, E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, S. aureus (MRSA), as well as the fungi C. neoformans and C. albicans. (The hazardous nature of many of these pathogens precludes developing simple assays that can be safely conducted in a regular undergraduate microbiology lab). D3 has taken advantage of CO-ADD resources in the past and the Cuban students were told that we planned to send to CO-ADD duplicate lots of all 22 compounds made by them in this workshop.

Lab Component of the Workshop In the lab phase of this Cuban workshop students (Figure 7) utilized the D3 Lab 2 procedure and Bill-Board equipment (shown in Scheme 3 and Figure 4) to synthesize many new acylated natural amino acids 4 to be tested as potential antimicrobial agents. 76 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 7. Lab Students and TAs. (see color insert)

As discussed earlier, two of the essential requirements for a D3 laboratory are: 1) Powerful, reproducible synthetic procedures to enable the synthesis of large numbers of potential drug molecules and 2) simple, inexpensive equipment to carry them out. All of the current D3 procedures are based on solid-phase combinatorial chemistry. The solid-phase nature enables multi-step syntheses to be successfully carried out with simple equipment on a micromole scale. The combinatorial aspect allows the creation of large catalogs of virtual molecules accessible by these D3 procedures. The students or student teams can then select target molecules from these catalogs and synthesize, using D3 procedures and equipment, 6 unique molecules at a time. Training of Our Undergraduate TAs To Lead the Laboratory Portion of the Workshop Two of our teaching assistants, PD and JS, in addition to being fluent in the Spanish language, were given extensive training by GS in D3 Lab 2 procedures at IUPUI prior to the workshop. Beginning in the summer months they personally completed the synthetic sequence two times and verified and optimized the chromatographic purification procedure for the control compound. In addition, PD and JS provided a complete translation of the laboratory procedure into Spanish, and the translated version was then successfully “beta-tested” by an independent IUPUI student who was also fluent in Spanish. JS and PD were each given the experience of preparing and distributing an isopycnic (neutral buoyancy) suspension of the starting resin, a prerequisite for even resin distribution to the individual reaction vessels, and they were provided with 1) a complete inventory of chemicals/equipment/supplies required for the workshop, 2) a complete set of reagent calculations, 3) a suggested order of tasks, 4) a detailed plan of multiple reagent preparation/distribution, 5) a sheet of adhesive, printed labels for the reagent vials, 6) an isopycnic preparation/distribution procedure complete with a photograph of the setup and 7) a compilation of key pre-lab remarks and suggestions for each session along with a listing of supplies/reagents/solvents needed for each session. 77 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

Our third teaching assistant, DT, was a student in AF’s D3 laboratory course at SCU and has since continued research in her independent laboratory optimizing procedures for new D3-compatible scaffolds. In addition, DT has served as an undergraduate TA for several organic chemistry labs at SCU. As such, he had extensive experience both with leading novice chemists in the lab and conducting solid-phase synthesis experiments.


D3 Lab Procedures and Layout For the Ernest Eliel Cuban Workshop we chose to utilize D3 Lab 2 because this lab involves the fewest number of steps of all our D3 procedures, makes use of readily available reagents, and teaches all the basic skills of solid-phase synthesis while students produce members of an important class of molecules with documented drug potential. The 24 students participating in the lab were assigned, in teams of two or three, to each of the 10 Bill-Boards. The combinatorial nature of D3 Lab 2 (Scheme 3) was carried out with two unique amino acids providing R1 in Row A or B, and three unique carboxylic acids as acylating agents R2 in Columns 1, 2 or 3 of the 2 x 3 grid of the Bill-Board. This affords six unique compounds in each Bill-Board. Reproducibility is a key requirement in the D3 program. This was demonstrated in two ways in the workshop laboratory: 1) As a control, every Bill-Board (and team) was assigned the same amino acids (phenylalanine = R1 in Row A, and tyrosine [protected as the t-butyl ether)] = R1 in Row B) and carboxylic acid (4-fluorobenzoic acid = R2) in Column 1. This meant that everyone should have synthesized phenylalanine 4-fluorobenzamide in position A1 and tyrosine 4-fluorobenzamide in position B1. Thus A1 and B1 are the “controls” (we already knew they would work) and can be used to guarantee the students obtain products (and satisfaction) if they properly carry out the synthetic procedures. 2) Throughout the lab different carboxylic acids R2 were used in columns 2 & 3, but each Bill-Board based on these different carboxylic acids was replicated by another Bill-Board team. In this way the four unique products produced in positions A2, A3 and B2, B3 are also replicated (actually duplicated in this case). For example, layouts illustrating replication at the control level of A1 and B1, and new derivatives in A2, A3, B2 B3 for replicated Bill-Boards 1 & 2, and 3 & 4, are shown in Figure 8.

Figure 8. Bill-Board Layout for Replicated Teams 1 & 2, and Replicated Teams 3 & 4. 78 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


This pattern of replication was done throughout the lab for rest of the remaining Bill-Board teams: 5 & 6; 7 & 8; 9 & 10, leading to ten lots of replicated compounds 1 (in every A1) and 4 (in every B1), and 2 lots each of the 20 new compounds in the other four Bill-Board positions A2, A3, B2 and B3. The total of 22 unique compounds made by the students are shown in Figure 9.

Figure 9. 22 Structurally Unique Compounds Made in Cuba Workshop.

Carrying Out the Lab Work Prior to the first lab the US student teaching assistants (TAs: PD, JS, and DT) distributed to each of the six reaction vessels in the ten Bill-Boards the resin-bound Fmoc amino acids phenylalanine and tyrosine (protected with a t-butyl group) in Rows A and B respectively. The first day the Cuban students carried out the deprotection (Fmoc removal) of the resin bound amino acids in Rows A and B, washed the resins, and added the assigned carboxylic acids (in previously prepared stock solutions containing catalyst hydroxybenzotriazole) to the appropriate columns, followed by coupling agent diisopropylcarbodiimide to all reaction vessels. For all these steps students followed a carefully written D3 Lab 2 procedure which had been extensively tested and verified by students at IUPUI and other schools in other global locations (Figure 10). In advance, the Cuban students were given the English version of the D3 Lab 2 procedure as well as a version PD and JS had translated into Spanish. 79 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 10. Carrying out D3 procedure (see color insert) The second day students extensively washed the resin in each of the six Bill-Board vessels and then cleaved the products from the resin with trifluoroacetic acid (TFA), draining the cleaved products into the individually tared and labeled product collection vials. They removed a 0.1 mL sample of product containing cleavage solution and placed it in an HPLC vial, completing their work for the second lab day. The TFA was evaporated from the 60 HPLC vials (10 Bill-Boards, 6 samples each) which were placed in a box and returned to IUPUI. GS subsequently analyzed the quality all 60 samples by LC/MS. The TFA/dichloromethane in the ten A1 collection vials from the 10 Bill-Board teams was evaporated overnight to provide samples, from all ten teams, of A1 for chromatographic purification the next day. The third afternoon students weighed the A1 collection vial from their BillBoard to calculate crude yields. They then chromatographed A1 on a simple 500 mg cyanosilica column, using a step-wise gradient eluent and collecting 1-2 mL fractions. The collected fractions were analyzed by TLC on a cyanosilica TLC plate and fractions containing only a single spot were combined into a tared vial. Typically the total volume of eluent was ~10 mL and product was collected in 1-3 fractions. These combined fractions were evaporated after the workshop was completed, weights recorded, and samples sent to Germany for NMR analysis. Post Workshop Follow-Up and Results 1) All 60 reaction products were analyzed by LC/MS at IUPUI. Results were sent back to Cuba for students to record and discuss. The crude A1 controls (10 samples from the 10 teams) had an average purity of 82% (range: 59-97%). For most of the 60 samples the crude purity was >70%. DMF was sometimes observed as a contaminant. It was present at 15-66% in eleven of the 60 samples, probably the result of incomplete washing of resin prior to the cleavage step. Reproducible purity among duplicate Bill-Boards was found to be variable, again often a function of contamination by DMF. 2) All product vials were evaporated to a film and weighed to calculate and record crude yield. 3) 1 mg samples of replicate lots of all 22 unique compounds were transferred to vials for CO-ADD antimicrobial testing. The vials used 80 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


were barcoded and were requested by GS, in advance, from CO-ADD. Prior to submission of the samples, an official CO-ADD spreadsheet was completed by GS and sent to CO-ADD. Once the spreadsheet was received by CO-ADD, Australian importation papers were provided by CO-ADD and were included with the samples. We are all eagerly awaiting the test results. 4) All ten A1 control products purified by the student teams were sent to Germany for NMR analysis. The spectrum obtained for one of them is shown in Figure 11 and is representative of the ten samples.

Figure 11. 1H Spectra of a Sample of A1 Purified by Students in Team 1 (Integration Cut Off for Display).

Assessment Goals The overall goal of this D3-based workshop was to integrate global chemistry education and drug discovery research into the University of Havana’s undergraduate instructional labs, exposing students to a compelling application of their learning as they prepare and test new compounds with drug potential against neglected diseases. The workshop also sought to build collaborations between Cuban and US scientists. In particular, D3 could benefit from the shared expertise of Professors Scott, O’Donnell, Fuller, Dounay and Rivera in education, drug discovery, combinatorial chemistry, solid-phase synthesis, and other synthetic approaches to bioactive molecules. These collaborations would further D3’s goal of finding drug leads for neglected diseases while building international partnerships in education and research. We hoped the common drug discovery goal would provide a natural environment to share and celebrate not just science and education, but also the cultural aspects of our unique backgrounds, both at an individual and societal level. How did we do? Scientific Exchange 1.

Eleven lectures and an active learning session were given by the faculty. Four Cuban students each gave 30 minute talks on their research. 81

Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

2.


3.

4.

Students successfully completed a three-step solid-phase synthesis. Each student team made six different molecules as they simultaneously carried out this sequence in six separate reaction vessels. With extensive replication, a total of 22 unique molecules were made and all of them were characterized by LC/MS. A subset was purified by chromatography and characterized by 1H NMR. Replicate samples of the crude products (almost all > 70% pure by LC/MS) were submitted to CO-ADD for evaluation of biological activity. Three hours were dedicated to more informal discussions of ongoing work and to developing ideas for possible future research connections. This time included proposals made by Cuban students to articulate innovative ideas that could be enabled by the D3 technology. A poster session was held in which Cuban and US students shared their research with one another and with faculty (Figure 12).

Figure 12. Student Poster Presentation. (see color insert)

Chemical Education: Dissemination of Knowledge and Equipment Curricular materials and equipment were demonstrated through the course of this workshop, and everything was left with the Cuban faculty and students for their future use. Specific materials shared included video lectures, written laboratory procedures (in English and Spanish), active learning library design exercises, a majority of physical equipment needed for the laboratory experiments, including the Bill-Board apparatus (quantity = 12), and surveys of student learning outcomes. Through the lectures, WS, AD, and AF conveyed three different applications of the D3 approach as it is implemented at their respective institutions. MO, in his absence, presented an audio/visual lectures teaching the mechanistic details of the steps in the D3 lab procedure. Through these presentations, the US faculty highlighted that the D3 laboratory idea can be tailored to the unique needs and strengths of a given institution. Moreover, this program welcomes innovations from new collaborators. Three US students (two of whom were fluent in Spanish) served as instructors for the laboratory portion of the workshop. They worked closely with Cuban students to introduce them to the use of the equipment and guided them through the procedures. Their familiarity with the course material as well as with the student perspective provided a rich dimension to the workshop. 82 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

Cultural Exchange: Ongoing Relationships, Planned Actions Rich relationships developed over the course of the week among students and faculty participating in the workshop. Activities outside of the workshop (e.g., at lunch, US-Cuban student outings) promoted candid interactions. Students exchanged email and Facebook contact information and intend to keep in touch with one another via social media. Faculty intend to continue ongoing research and educational collaborations via email, phone, and Skype.


Cuban Student Perspectives and Reflections We surveyed the Cuban students with several questions. Responses in Spanish were translated into English. Here is a sampling of Cuban students’ reflections and perspectives prompted by these questions. Please comment on how your understanding of the subject has changed as a result of this workshop. •

•

“With this workshop, I was able to better understand the complete process [of drug discovery], from the onset of an idea, to the medicine getting put into the market.” “I had never approached solid phase synthesis because it was not related to my research. However, though this workshop, I have been able to understand why organic reactions are completed in the solid phase and the concept of combinatorial chemistry, as well as the importance of curing neglected diseases. I can better understand the process of conducting chemical reactions.”

Please comment on what skills you have gained as a result of this class. •

“Skills in working with the Bill-Board and combinatorial synthesis.”

Please comment on how this class has changed your attitudes toward chemistry. • • •

•

“It [The workshop] has motivated me to take additional chemistry courses and expand my knowledge of solid phase synthesis.” “This workshop has increased my interest in chemistry because of its application to combating 3rd world diseases.” “This workshop showed me how chemistry can be very useful in helping humanity. It has motivated me to do research in the field of neglected disease.” “It [The workshop] has motivated me to take additional chemistry courses and expand my knowledge of solid phase synthesis.”

What will you carry with you into other classes or other aspects of your life? 83 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

• •

“The use of the Bill-Board and the incentive of discovering new medications.” “A new vision. Because this is an innovative project, we can take part of a big research project.”

Please comment on how the instructional approach to this workshop helped your learning. •


•

“The exchange of students and professors was very important and beneficial.” “This workshop was help to improve my ideas about drug discovery of neglected disease and in the application of combinatorial chemistry on solid phase.”

Please comment on how the workshop activities helped your learning. • •

•

“It helped improve my understanding of English and understanding of peptide synthesis.” “By listening to the presentations I could better understand solid phase reactions and the experimental work allowed me to put in practice the knowledge I acquired.” “The best is working in groups, because we can learn from each others. Other really good thing is that professors were at the lab together with students and instructors.”

We also conducted post-workshop surveys soliciting student impressions, rated on a scale of 1 to 5, of the efficacy of selected workshop elements on their learning. Some of the most strongly consistent responses (>4.5, N=20, standard deviation from .28 to .87. Scale: 5 = great gain; 4 = good gain; 3 = moderate gain; 2 = a little gain; 1 = no gain.) indicated an increase in: • • • • • •

Understanding why it is challenging to cure "neglected" diseases. Understanding the conceptual application of combinatorial chemistry. Understanding how studies done in this workshop address real world issues. Ability to integrate information from lectures to understand new reaction mechanisms in the laboratory. Enthusiasm for chemistry. Confidence they could contribute to chemistry research.

Students said their interactions with other participants, together with the experimental work, greatly assisted learning. It was gratifying that student responses were overwhelmingly and uniformly positive. Although we recognize that self-reported information on student learning does not represent the most accurate way to evaluate student learning outcomes, we are encouraged by the positive responses in this initial workshop endeavor. Here are two samples of Cuban students’ reflections on their workshop experience: 84 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


“The symposium of the D3 project was an exceptional experience, where we learned a lot about neglected diseases and the actual way to develop drugs for treating them. We had the opportunity of sharing knowledge and opinions with students from Colorado Collage, IUPUI and Santa Clara University. I think it is remarkable what they are doing in this project, paying attention to such neglected diseases, which are the cause of millions of deaths in the word. I hope other universities join to this project, as University of Havana have done.” (Dayan Viera Barredo, Undergraduate student of Chemistry, 4th year) “The D3 workshop was a great opportunity for the exchange of science and culture between the two countries. During that week, I learned about not only combinatorial chemistry and how to use a billboard instrument, but also I learned about American people.” (Ana C. Rodríguez Humpierre Undergraduate student of Chemistry, 5th year) US Student Perspectives and Reflections The three US students that accompanied us, PD and JS from IUPUI, and DT from Santa Clara University (Figure 13), provided a crucial resource technically, personally and culturally - for the successful implementation of the Cuban workshop.

Figure 13. USA Student TAs Relaxing (see color insert) Their student status, role as teaching assistants with expertise in D3 laboratory procedures (coupled with their ability to communicate in Spanish) enabled them to make strong links scientifically and personally to Cuban students and their culture. It was a life changing experience for them. What follows, in their own words, are reflections from each of them regarding their workshop experience:

Priya Dave (IUPUI) Like many other Americans, my views on Cuba before visiting had been shaped by the media and from what I had studied in history textbooks. Cuba supposedly was an impoverished country without access to proper resources. Going to Cuba as an American, I felt a little uneasy when thinking about the tense political backdrop that seemed to overshadow our government’s relations 85 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


- I couldn’t help but think about what the Cuban students would think about Americans. What were they taught in their history textbooks and what did their news channels broadcast? Our first full day in Havana I quickly learned my perspective on Cuba was incorrect in many ways. Cuba was far from a third world country I had imagined – it had an almost non-existent unemployment rate, incredible education system, and not to mention low crime rate. It was refreshing to see the lack of American influence. There were no McDonald’s or Starbucks, or name brand hotels crowding the streets of the city. Instead the restaurants, architecture, and cars lining the roads were of their own distinct style. The first day, as we American students walked into the chemistry lab, we couldn’t help but notice all of the differences. Most striking was that there were only two small fume hoods in the center of the laboratory and the rest of the benches were empty spaces. A common theme throughout the week was working with what we had. And that is exactly what we did - we improvised. The Cuban students were already used to doing this. In fact, at any given step, the students would be thinking about how they could alter the procedure or if there wasn’t enough equipment, what to use instead. It was incredible to witness how they worked, using the procedure as a template instead of following it word by word. I could tell that all students had a solid understanding and passion for chemistry! Preparing for the Cuban lab began several months before embarking. As part of my Spanish service learning class, I began translation of an introductory video from English to Spanish. Afterwards, Juan and I together split translation of the actual chemistry procedure. Translation took hours and it was a challenging process! We even had to alter some of the script’s content to better suit a Cuban audience. Preparation also involved running several trials of the D3 procedure, synthesizing many novel potential drugs, and learning about the process of drug discovery. Additionally, after translation of the script, two students familiar with Spanish came in to test the procedure, which was ultimately successful! Overall, the most incredible aspect about travelling abroad with Distributed Drug Discovery was being able to connect with students. As a Spanish student, I had studied abroad with American university students for short periods of time, but there was nothing quite like the insights we were able to make through meeting and working with students from another culture. The students opened up their worlds to us. We got a flavor of their lives. They took us to their favorite outdoor pizza shop, and a whimsical local ice cream parlor. We went to a quiet, serene beach and explored the best views of the city! Ultimately, they were just as fascinated about our way of life in the U.S. as we were about Cuba. As a humanities major, I recall when I told the students, “I’m studying humanities, but after that I will go to medical school.” They looked at me in shock and multiple students asked me, “Can you really do that?” In Cuba, right out of high school students pick a career. I was just as fascinated by the fact that in Cuba all students get free education. In the United States, many more people would take advantage of a college education if it were free! But in fact, Cuba presents the contrary. The reality is that even with a degree in a lucrative field, such as medicine or chemistry, 86 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

students do not get paid for the amount they work. Many Cubans find it more practical to work in the tourism industry, giving tours of the city or working in the restaurants instead. If I had one word to describe Cuba, it would be genuine. The students were genuinely passionate about what they were doing. They were extremely inviting, ensuring that we were always having a good time. They spent their time with us each night, showing us the city. The experience left me with a new perspective on Cuba and a great appreciation for the Cuban values, culture, and people.


Juan Sanchez (IUPUI) I was busy enough preparing for the trip that I did not have time to form expectations about it, so I just decided to go with the flow and let every bit of this experience surprise me. I had prepared over the summer by learning all the steps of the procedure and how to use the equipment, so by the time the trip came around I was confident that everything would go well. Geno did an excellent job of labeling the equipment we were going to use. This made the preparations of the reagents for the workshop efficient, and gave us time to solve other issues in the setup of the lab at the University of Havana. It was an enjoyable challenge to use my language skills to translate the procedure from English to Spanish. We had worked long, hard hours to complete a procedure that had clear instructions in the students’ native language about how to proceed in the lab. I wanted to hear the opinions of the students regarding the translated procedure. The laboratory facility that we used at University of Havana was by no means state of the art. However, it was inspiring to see how the students and professors had the talent to look around the lab and create the best conditions possible for us to set up the lab for the workshop. I will never forget the moment when I realized that all of the students and professional chemists we had met decided to become chemists because it was what they truly felt passionate about. In Cuba many professions are not well compensated, but many people choose them over working in tourism where they can earn much more, because their genuine passion for what they do is worth more to them than money. Even though they lack the equipment and facilities that we take for granted, they still are able to do the lab work and learn, and they still become great chemists. That week we connected so well with the students in part because they were open and friendly, but also because they shared our passion for learning no matter the monetary compensation. One of the most impactful things I saw in this trip was the genuine love that all the students have for chemistry. All the time that they spend studying chemistry is a labor of love, and not for the money. It was upsetting to realize that there are passionate and driven students in Cuba but they do not have the resources to reach their full potential. A lot of their work is delayed because they send samples outside the country to be analyzed, whereas we have the facilities, such as an LC/ MS and NMR, that enable us to get results in a few hours. Having the opportunity to interact with the students made me hope for a normalized relationship between 87 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

our two countries. I hope that we can find ways to have future collaborations with passionate Cuban scientists who are also fully equipped to do the work to the best of their potential. Havana was beautiful, but its beauty was enhanced by the wonderful professors and students who hosted us. They were generous enough with their time to show us their daily lives and tour us around the city. Many friendships were made the week we were there. We are already planning a trip to visit them in the near future. I would love to visit my new friends and also see other parts of Cuba.


Daniel Tiano (Santa Clara University) As a student who regrettably decided not to study abroad when I had the opportunity, one can imagine the surprise and joy I felt when I was offered an opportunity to participate in the Ernest Eliel U.S.-Cuba Collaborative Workshop. My love for teaching and desire to do something meaningful in the world made it an easy choice to go. When I arrived at the hotel on the first day, I admittedly felt a little nervous about the workshop. What if my Spanish accent is too horrendous to understand? What if things don’t go smoothly in lab? How will I be received by the University of Havana Chemistry Department? My apprehensions were immediately laid to rest after the first day of the workshop. I remember having friendly, relaxed conversations with the Cuban students/faculty from the get-go; one of the first conversations I had with one of them was about American and Cuban television. The Cuban students/faculty continued to shower me with hospitality throughout the week. I had dinner at the department chair’s house twice, went to lunch with the students/faculty nearly every day, and even went on a late-night adventure with them to Christ of Havana! In addition to the casual outings and activities, I was also able to talk with the Cubans on a deeper level about things like how they perceive America vs. individual Americans, their thoughts on the relationship between the U.S. and Cuba, and what they thought about their country’s leadership. Of all the ways this trip shaped my world view, the one I value most is the exchange of opinions and ideas I was able to participate in. Believe it or not, I was able to do some actual work in addition to all the fun I had! While the American professors gave lectures and prepared the Cubans for the lab, the other American students and I prepared the lab materials and oversaw the procedure as TA’s. We had all done a variation of the procedure before, which allowed us to troubleshoot and catch mistakes before they happened. One of the things that surprised me the most about the whole trip was how little the Cubans had to work with in the lab equipment-wise. Each person got one or two pairs of gloves to use for the entire day (entire week). There was only one working hood, which forced twenty-something students to work with volatile chemicals in the open lab. There were unsecured air tanks in the corner of the lab. There weren’t any hotplates, so we heated a sample using a propped-up hair dryer. The way the Cubans made do with their limited resources was eye-opening and humbling, 88 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

especially coming from a place where I can use several pairs of gloves in one lab session without thinking twice. Needless to say, I would miss another week of school in a heartbeat to go to Cuba again.

Plans for Future Collaborations


Research Collaborations We had discussions during the day and after hours regarding possible future collaborations among US faculty and between US and Cuban faculty and students. Some specific project ideas are summarized below. Two proposals emerged from the laboratory of DR that build on their expertise in multi-component reactions. One proposed access to many analogs of metallopeptidase inhibitors, and the other to multiple analogs of putative angiotensin converting enzyme (“ACE”) inhibitors. Cuban students will work to develop robust and reproducible procedures for these experiments that can be applied in other laboratories. Once they have developed these, students and faculty at US institutions, including SCU, IUPUI, and CC, will replicate the results to validate the procedures and make new analogs. WS and MO proposed a new D3 lab that would merge their published solid-phase unnatural amino acid synthesis procedure with DR’s published Ugi functionalization of resin-bound amino acids. This would be optimized and reproducibly validated in a joint IUPUI/University of Havana collaboration, possible carried out at IUPUI by a student on a short term exchange from the University of Havana. AD had presented ongoing work exploring greener approaches for chemistry currently utilized by D3, including comparisons of solution phase and solid phase synthesis techniques and explorations of replacing more hazardous and expensive solvents with less expensive and milder options. To enable cross-site replication of promising procedures and undertake new initiatives on this front, AF will incorporate similar projects into SCU laboratory courses. Discussions will continue between DR and AD centered in particular on sharing more ideas about their common interests in developing anti-parasitic compounds. All US faculty reiterated their willingness to serve as a resource for cross-site replications and validations of procedures. WS invited DR to visit the United States after the workshop. In November of 2016 DR visited the campuses of both IUPUI and Notre Dame for discussions and talks with scientists, students, and officials connected to offices of international activities. He gave an invited lecture on his work to scientists at Eli Lilly but was unable to have exchanges with Lilly scientists because of the ongoing Cuban embargo. In addition to the science and educational exchanges he had while in the US DR was present to witness the United States vote on its next president. After the election he traveled to the nation’s capital in Washington DC to have discussions with officials of the American Chemical Society. 89 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

Distributed Drug Discovery Dissemination The faculty expressed a common interest in identifying strategies to disseminate the central ideas of D3 more broadly and to engage more collaborators globally. US faculty will publicize the participation of students and faculty in this workshop within their institutions and, when possible, through local media channels. The workshop faculty are outlining a strategy for enhancing the visibility of the D3 program within the broader scientific community, including publications and presentations at conferences.


Final Thoughts As we worked together conducting the “Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery” we gained a richer understanding of why chemistry is often referred to as “The Central Science”. Over a one week period we educated students in fundamental chemistry knowledge and skills and showed them how essential this understanding is to addressing the critical need for drugs to treat neglected diseases. While they learned about the central role of chemistry in the complex of disciplines required for drug discovery they took part in that process by making many new molecules that are being tested for their potential as antimicrobial agents. In addition, as we built trust and comradery working together on shared scientific goals we learned about each other and our respective cultures in a natural and unselfconscious way. We saw chemistry as a “Central Science” that went beyond its role in scientific research and discovery to being a universal medium for breaking down geographic and cultural boundaries. We believe if Ernest Eliel could have witnessed Cuban and United States educators and students working together in this workshop, named in his honor, he would have seen his legacy in operation and had a broad smile on his face!

References 1. 2.

3.

4.

Scott, W. L. Distributed Drug Discovery. Department of Biochemistry, Seminar, Jagiellonian University, Krakow, Poland, April 7, 2003. O’Donnell, M. J.; Scott, W. L. Distributed Discovery in the Undergraduate Organic Lab: Combinatorial Solid-Phase Synthesis of Amino Acid Derivatives. 18th Biennial Conference on Chemical Education (BCCE); Symposium (Invited): “Combinatorial Chemistry in the Undergraduate Curriculum,” Iowa State University; Ames, IA; July 21, 2004. Scott, W. L.; O’Donnell, M. J. Distributed Drug Discovery, Part 1: Linking Academia and Combinatorial Chemistry to Find Drugs for Developing World Diseases. J. Comb. Chem. 2009, 11, 3–13. Scott, W. L.; Alsina, J.; Audu, C. O.; Babaev, E.; Cook, L.; Dage, J. L.; Goodwin, L. A.; Martynow, J. G.; Matosiuk, D.; Royo, M.; Smith, J. G.; Strong, A. T.; Wickizer, K.; Woerly, E. M.; Zhou, Z.; O’Donnell, M. J. Distributed Drug Discovery, Part 2: Global Rehearsal of Alkylating Agents 90 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

5.


6.

7.

8.

9.

10.

11.

12.

13.

14. 15.

16.

for the Synthesis of Resin-Bound Unnatural Amino Acids and Virtual D3 Catalog Construction. J. Comb. Chem. 2009, 11, 14–33. Scott, W. L.; Audu, C. O.; Dage, J. L.; Goodwin, L. A.; Martynow, J. G.; Platt, L. K; Smith, J. G.; Strong, A. T.; Wickizer, K.; Woerly, E. M.; O’Donnell, M. J. Distributed Drug Discovery, Part 3: Using D3 Methodology to Synthesize Analogs of an Anti-Melanoma Compound. J. Comb. Chem. 2009, 11, 34–43. Scott, W. L.; Denton, R. E.; Marrs, K. A.; Durrant, J. D.; Samaritoni, J. G.; Abraham, M. M.; Brown, S. P.; Carnahan, J. M.; Fischer, L. G.; Glos, C. E.; Sempsrott, P. J. Distributed Drug Discovery: Advancing Chemical Education through Contextualized Combinatorial Solid-Phase Organic Laboratories. J. Chem. Educ. 2015, 92, 819–826. Scott, W. L.; O’Donnell, M. J. Solid Phase Synthesis and an Introduction to Combinatorial Chemistry; NSF Workshop; Ketcha, D. M., Taylor, R. T.; Miami University, Miami, OH, July 27−August 1, 2003. Scott, W. L.; Denton, R. E.; Samaritoni, J. G.; Marrs, K. A.; O’Donnell, M. J. International Distributed Drug Discovery (D3) Workshop; Indiana University Purdue University Indianapolis, July 22−26, 2013. O’Donnell, M. J.; Durrant, J. D.; Denton, R. E.; Marrs, K. A.; Samaritoni, J. G.; Scott, W. L. A Sophomore Organic Lab Research Experience in the Context of Distributed Drug Discovery (D3) for Neglected Diseases; BCCE – Biennial Conference on Chemical Education (BCCE), Workshop, Grand Valley State University, MI, August 3−7, 2014. In 2004 WLS conducted other one-week workshops at the University of Barcelona (Spain), Medical University of Lublin (Poland) and Moscow State University (Russia). Scott, W. L.; Samaritoni, J. G.; O’Donnell, M. J.; Dounay, A. B.; Fuller, A. A.; Dave, P.; Sanchez, J. M.; Tiano, D. G.; Rivera, D. G. Ernest Eliel Workshop – US and Cuba Collaboration in Chemistry Education and Neglected Disease Drug Discovery, University of Havana, Havana, Cuba, October 17−21, 2016. O’Donnell, M. J. The Preparation of Optically Active a-Amino Acids from the Benzophenone Imines of Glycine Derivatives. Aldrichim. Acta 2001, 34, 3–15. O’Donnell, M. J. The Enantioselective Synthesis of a-Amino Acids by PhaseTransfer Catalysis with Achiral Schiff Base Esters. Acc. Chem. Res. 2004, 37, 506–17. O’Donnell, M. J.; Zhou, C.; Scott, W. L. Solid-Phase Unnatural Peptide Synthesis (UPS). J. Am. Chem. Soc. 1996, 118, 6070–6071. Scott, W. L.; Martynow, J. G.; Huffman, J. C.; O’Donnell, M. J. Solid-Phase Synthesis of Multiple Classes of Peptidomimetics from Versatile Resin-Bound Aldehyde Intermediates. J. Am. Chem. Soc. 2007, 129, 7077–7088. Scott, W. L.; Zhou, Z.; Martynow, J. G.; O’Donnell, M. J. Solid-Phase Synthesis of Amino- and Carboxyl-Functionalized Unnatural -Amino Acid Amides. Org. Lett. 2009, 16, 3558–3561. 91

Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


17. Samaritoni, J. G.; Copes, A. T.; Crews, D. K.; Glos, C.; Thompson, A. L.; Wilson, C.; O’Donnell, M. J. Unexpected Hydrolytic Instability of N-Acylated Amino Acid Amides and Peptides. J. Org. Chem. 2014, 79, 3140–3151. 18. Scott, W. L.; Brown, S. P.; Audu, C.; Samaritoni, J. G.; Sempsrott, P. J.; Strong, A. T.; Zhou, Z.; O’Donnell, M. J. Distributed drug discovery: Unnatural amino acid amides. 238th ACS National Meeting, Washington, DC, August 16, 2009, Poster, ORGN 455. 19. Scott, W. Distributed Drug Discovery (D3): Linking basic research and education to find drug leads for neglected diseases. 240th ACS National Meeting, Boston, MA, August 23, 2010, Oral, BMGT 16. 20. Scott, W. L.; O’Donnell, M. J. Distributed drug discovery (D3): Enabling computational and synthetic chemists to work together to educate students while discovering drugleads for neglected diseases. 243rd ACS National Meeting, San Diego, CA, March 25, 2012, Oral, COMP 91. 21. Crews, D. K.; Samaritoni, J. G.; Scott, W. L.; O’Donnell, M. J. Solid phase synthesis of Nacylated amino acid amides using Rink resin. 245th ACS National Meeting, New Orleans, LA, April 7, 2013, Poster, CHED 957. 22. Scott, W. L.; Anderson, G. G.; Denton, R. E.; Harper, R. W.; Marrs, K. A.; Samaritoni, J. G.; O’Donnell, M. J. Distributed Drug Discovery (D3): Advancing chemical education through contextualized organic laboratories. 246th ACS National Meeting, Indianapolis, IN, September 10, 2013, Oral, CHED 344. 23. O’Donnell, M. J.; Abraham, M. M.; Anderson, G. G.; Carnahan, J. M.; Coffey, B. M.; Denton, R. E.; Harper, R. W.; LaCombe, J. M.; Marrs, K. A.; Samaritoni, J. G.; Scott, W. L. Distributed Drug Discovery (D3): Contextualized educational laboratory program in chemistry and biology toward inhibiting biofilm formation related to cystic fibrosis. 246th ACS National Meeting, Indianapolis, IN, September 11, 2013, Oral, CHED 397. 24. Denton, R. E.; Abraham, M. M.; Callahan, C. A.; Cankarova, N.; Carnahan, J. M.; Cerninova, V.; Copes, A.; Fortunak, J. M.; Harper, R. W.; Popiolek, L.; Samaritoni, J. G.; Soural, M.; Thompson, R.; Tomanova, M.; O’Donnell, M. J.; Scott, W. L. Distributed Drug Discovery (D3): Developing national and international distributed educational processes and standards in the context of identifying anti-malarial lead compounds. 246th ACS National Meeting, Indianapolis, IN, September 11, 2013, Oral, CHED: 398. 25. Scott, W. L.; Denton, R. E.; Harper, R. W.; Samaritoni, J. G.; O’Donnell, M. J. Distributed drug discovery (D3): Virtual D3 biomimetic catalogs, tested molecules, hit follow-up, drugs. 246th ACS National Meeting, Indianapolis, IN, September 8, 2013, Oral, MEDI 20. 26. Abraham, M. M.; LaCombe, J. M.; Anderson, G. G.; Carnahan, J. M.; Coffey, B. M.; Denton, R. E.; Harper, R. W.; Marrs, K. A.; Samaritoni, J. G.; Scott, W. L.; O’Donnell, M. J. Distributed drug discovery (D3): Successful integration of D3 components. Undergraduate computational, synthetic, and biological evaluation of phenylalanine derivatives as potential biofilm inhibitors. 246th ACS National Meeting, Indianapolis, IN, September 9, 2013, Poster, CHED 195. 92 Cheng et al.; Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


27. Carnahan, J. M.; Samaritoni, J. G.; Crews, D. K.; Krchnak, V.; Lawrence, B. M.; Scott, W. L.; O’Donnell, M. J. Distributed drug discovery (D3): Saponification of N-acylated L-phenylalanine from Wang or Merrifield resin. Assessment of cleavage efficiency and epimerization. 246th ACS National Meeting, Indianapolis, IN, September 9, 2013, Poster, CHED 273. 28. Fischer, L. G.; Glos, C. E.; Lopez, D.; Samaritoni, J. G.; Stickney, K. W.; O’Donnell, M. J.; Scott, W. L. Distributed drug discovery (D3): Facilitating research and collaboration through an undergraduate combinatorial chemistry course that led to the discovery and follow up of a molecule affecting the oxytocin receptor. 246th ACS National Meeting, Indianapolis, IN, September 8, 2013, Poster, CHED 72. 29. Samaritoni, J. G.; Crews, D.; Glos, C. E.; Thompson, A. L.; Wilson, C.; Martin J. O’Donnell, M. J.; William L. Scott, W. L. Unexpected hydrolytic instability of N-acylated amino acid amides and peptides. 246th ACS National Meeting, Indianapolis, IN, September 11, 2013, Poster, ORGN 545. 30. Pruett, C. H.; Collins, A. D.; Scott, W. L.; O’Donnell, M. J.; Hopkins R. B. Application of distributed drug discovery methodology to the synthesis of some analogs of antimalarial screen hits. 247th ACS National Meeting, Dallas, TX, March 17, 2014, Poster, CHED 935. 31. Scott, W. L.; Samaritoni, J. G.; Anderson, G.; Marrs, K.; Colglazier, S.; Hitchens, J.; Burris, S.; Ware, M.; O’Donnell, M. J. Distributed drug discovery (D3) in action: Finding inhibitors of P. aeruginosa. 252nd ACS National Meeting, Philadelphia, PA, August 24, 2016, Oral, MEDI 275. 32. Scott, W. L. Samaritoni, J. G.; Popiolek, L.; Dounay, A.; Schirch, D.; Garcia Rivera, D.; Biernasiuk, A.; Malm, A.; O’Donnell, M. J. Distributed drug discovery (D3) update: First global student collaboration in neglected disease discovery. 252nd ACS National Meeting, Philadelphia, PA, August 24, 2016, Oral, CHEM 412. 33. Fuller, A. A. Combinatorial Solid-Phase Synthesis of Aromatic Oligoamides: A Research-Based Laboratory Module for Undergraduate Organic Chemistry. J. Chem. Educ. 2016, 93, 953–957. 34. Polypropylene Bill-Board, drain trays, collection trays and other associated supplies from Chemglass: Catalog #CG-1869. http://www.chemglass.com/ pages/billboards.asp (accessed April 20, 2017). 35. For a recent review, see: Sun, J.; Zuckermann, R. N. Peptoid Polymers: A Highly Designable Bioinspired Material. ACS Nano 2013, 7, 4715–4732. 36. Zuckermann, R. N.; Kerr, J. M.; Kent, S. B. H.; Moos, W. H. Efficient Method for the Preparation of Peptoids [Oligo(N-Substituted Glycines)] by Submonomer Solid-Phase Synthesis. J. Am. Chem. Soc. 1992, 114, 10646–10647. 37. Huang, M. L.; Benson, M. A.; Shin, S. B. Y.; Torres, V. J.; Kirshenbaum, K. Amphiphilic Cyclic Peptoids that Exhibit Antimicrobial Activity by Disrupting Staphylococcus aureus Membranes. Eur. J. Org. Chem. 2013, 3560–3566.



38. Lee, B.-C.; Chu, T. K.; Dill, K. A.; Zuckermann, R. N. Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer. J. Am. Chem. Soc. 2008, 130, 8847–8855. 39. Robertson, E. J.; Battigelli, A.; Proulx, C.; Mannige, R. V.; Haxton, T. K.; Yun, L.; Whitelam, S.; Zuckermann, R. N. Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets. Acc. Chem. Res. 2016, 49, 379–389. 40. Alluri, P. G.; Reddy, M. M.; Bachhawat-Sikder, K.; Olivos, H. J.; Kodadek, T. Isolation of Protein Ligands from Large Peptoid Libraries. J. Am. Chem. Soc. 2003, 125, 13995–14004. 41. Fuller, A. A.; Yurash, B. A.; Schaumann, E. N.; Seidl, F. J. Self-Association of Water-Soluble Peptoids Comprising (S)-N-1-(Naphthylethyl)glycine Residues. Org. Lett. 2013, 15, 5118–5121. 42. Fuller, A. A.; Holmes, C. A.; Seidl, F. J. A Fluorescent Peptoid pH-Sensor. Biopolymers (Peptide Science) 2013, 100, 380–386. 43. Fuller, A. A.; Seidl, F. J.; Bruno, P. A.; Plescia, M. A.; Palla, K. S. Use of the Environmentally Sensitive Fluorophore 4-N,N-Dimethylamino-1,8naphthalimide to Study Peptoid Helix Structures. Biopolymers (Peptide Science) 2011, 96, 627–638. 44. Hjelmgaard, T.; Faure, S.; De Santis, E.; Staerk, D.; Alexander, B. D.; Edwards, A. A.; Taillefumier, C.; Nielsen, J. Improved Solid-Phase Synthesis and Study of Arylopeptoids with Conformation-Directing Side Chains. Tetrahedron 2012, 68, 4444–4454. 45. Aditya, A.; Kodadek, T. Incorporation of Heterocycles into the Backbone of Peptoids to Generate Diverse Peptoid-Inspired One Bead One Compound Libraries. ACS Comb. Sci. 2012, 14, 164–169. 46. Kodadek, T.; McEnaney, P. J. Towards Vast Libraries of Scaffold-Diverse, Conformationally Constrained Oligomers. Chem. Commun. 2016, 52, 6038–6059. 47. Anastas, P. T.; Warner, J. C. Green Chemistry: Theory and Practice; Oxford University Press: New York, 1998; p 30. 48. https://www.acs.org/content/acs/en/greenchemistry/what-is-greenchemistry/principles/12-principles-of-green-chemistry.html (accessed April 20, 2017). 49. O’Donnell, M. J. D3 Lab 2: Reaction Mechanisms for Fmoc-Deprotection, N-Acylation and Resin Cleavage. https://iu.mediaspace.kaltura.com/ media/D3+Deprotect+Acylate+Cleave+Mech+Tutorial+O%27Donnell/ 1_k0tzmfv7 (accessed: April 20, 2017).


Ernest Eliel Workshop â US and Cuba Collaboration in Chemistry

Recommend Documents

Ernest Eliel Workshop â US and Cuba Collaboration in Chemistry