Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs

Multi-Institution Research and Education Collaboration Identifies New Antimicrobial Compounds

New antibiotics are urgently needed to address increasing rates of multidrug resistant infections. Seventy-six diversely functionalized compounds, comprising five structural scaffolds, were synthesized and tested for their ability to inhibit microbial growth. Twenty-six compounds showed activity in the primary phenotypic screen at the Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up testing of active molecules confirmed that two unnatural dipeptides inhibit the growth of Cryptococcus neoformans with a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses were carried out by undergraduate students at five schools implementing Distributed Drug Discovery (D3) programs. This report showcases that a collaborative research and educational process is a powerful approach to discover new molecules inhibiting microbial growth. Educational gains for students engaged in this project are highlighted in parallel to the research advances. Aspects of D3 that contribute to its success, including an emphasis on reproducibility of procedures, are discussed to underscore the power of this approach to solve important research problems and to inform other coupled chemical biology research and teaching endeavors.

(S)-2-[(4-Fluorophenyl)formamido]-3-phenylpropanoic acid

The crystal structure exhibits monoclinic (P2₁) symmetry at room temperature. The two mol­ecules in the asymmetric unit of the title compound, C₁₆H₁₄FNO₃, exhibit different torsion angles along the central sp³ C—N bonds and are linked together through two N—H⋯O hydrogen-bonding inter­actions.

The title compound, C₁₆H₁₄FNO₃, was synthesized via solid phase methods; it exhibits monoclinic (P2₁) symmetry at room temperature. The two independent mol­ecules that comprise the asymmetric unit display distinct torsion angles of 173.2 (2) and 72.6 (2)° along the central sp³ C—N bond. In the crystal, hydrogen bonding through N—H⋯O contacts couples the asymmetric unit mol­ecules into pairs that align in layers extending parallel to (100) via additional O—H⋯O inter­actions. The phenyl ring of one independent mol­ecule was found to be disordered over two sets of sites in a 0.55 (3):0.45 (3) ratio.

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein–ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.

Innovations in Undergraduate Chemical Biology Education

Chemical biology derives intellectual vitality from its scientific interface: applying chemical strategies and perspectives to biological questions. There is a growing need for chemical biologists to synergistically integrate their research programs with their educational activities to become holistic teacher-scholars. This review examines how course-based undergraduate research experiences (CUREs) are an innovative method to achieve this integration. Because CUREs are course-based, the review first offers strategies for creating a student-centered learning environment, which can improve students' outcomes. Exemplars of CUREs in chemical biology are then presented and organized to illustrate the five defining characteristics of CUREs: significance, scientific practices, discovery, collaboration, and iteration. Finally, strategies to overcome common barriers in CUREs are considered as well as future innovations in chemical biology education.