- Email: [email protected]
Reaction: Broad-Spectrum Antibiotics, a Call for Chemists
derivatives by using a purely synthetic path, hence designating semi-synthesis as the favorable and commonly used path for the improvement of naturalproduct-based antimicrobial drugs. R&D of novel antimicrobial agents is based on either target-based rational design or HTS of libraries of compounds covering broad chemical spaces. A prerequisite of rational design aimed at the development of an entirely new antimicrobial agent or the improvement of existing drugs through chemical derivation is access to detailed molecular-level information on the mechanism of desired activity, side effects, or resistance. For example, the elucidation of the structures of the bacterial ribosome and of a large collection of ribosome-targeting antibiotics in complex with their ribosomal target sites by the groups of Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath, who were awarded the Nobel Prize in Chemistry in 2009, revolutionized the rational design of novel bacterial ribosome-targeting antibiotics.10 These structures shed light on the fine details of drug binding sites and also revealed new and unique sites that can be targeted with rationally designed, novel types of antibacterial agents and thereby opened numerous new opportunities for the development of antibacterial drugs. Necessary for high-throughput drug discovery is improving the capability to prepare large numbers of novel small molecules and generate libraries that will cover a large swath of existing and novel chemical spaces. In the last few decades, diversity-oriented synthesis (DOS) has evolved as an important concept for the generation of unique small-molecule libraries. DOS is aimed at the development of highly efficient synthetic pathways requiring a minimum number of efficient chemical transformations that will yield molecular skeletons that can be structurally defined by specific and unique coordinates in the chemical space.11 To
10
enable a facile drug lead-optimization process, skeletons generated by the DOS approach should contain functional groups that enable derivation by the attachment of substituents in a site- and chemo-selective manner. By granting efficient access to unexplored regions of chemical space, the concept of DOS, fueled by creative ideas of organic chemists worldwide, is likely to continue to play an important role in re-enriching the pipeline with new antimicrobial drugs. To conclude, the complexity of the task of regenerating the currently sparse pipeline of antimicrobial drugs has put the development of synthetic methodologies for antimicrobial drug R&D under the spotlight given that the current synthetic methodologies are not at the point of perfection. Chemical research must focus on devising new and improved methodologies with an emphasis on synthetic efficiency, expanding the chemical spaces searched, and ensuring a feasible process for industrial-scale production of the new antimicrobial drugs that emerge from the pipeline. Although outstanding progress has been made in organic chemistry during the last century, the field is very far from the point at which it can rest on its laurels. Chemists should aspire to construct diverse molecular scaffolds of all levels of structural complexity from basic and inexpensive starting materials through a series of chemical transformations that provide full control over enantio-, regio-, and chemo-selectivity. This goal will be achieved through creativity, improved synthetic methodologies, and importantly, a focus on the development of novel reactions for the formation and cleavage of chemical bonds. With an increase in funding and research focus in the near future, the development of novel synthetic tools in combination with the identification and structural characterization of novel microbial drug targets will undoubtedly put antimicrobial drug R&D back on the right
Chem 3, 8–14, July 13, 2017 ª 2017 Published by Elsevier Inc.
track and enable mankind to gain the upper hand in combating microbial infections in the future. 1. Armelagos, G.J., Brown, P.J., and Turner, B. (2005). Soc. Sci. Med. 61, 755–765. 2. Laxminarayan, R., Duse, A., Wattal, C., Zaidi, A.K., Wertheim, H.F., Sumpradit, N., Vlieghe, E., Hara, G.L., Gould, I.M., Goossens, H., et al. (2013). Lancet Infect. Dis. 13, 1057–1098. 3. Davies, J., and Davies, D. (2010). Microbiol. Mol. Biol. Rev. 74, 417–433. 4. Goff, D.A., Kullar, R., Goldstein, E.J.C., Gilchrist, M., Nathwani, D., Cheng, A.C., Cairns, K.A., Escando´n-Vargas, K., Villegas, M.V., Brink, A., et al. (2017). Lancet Infect. Dis. 17, e56–e63. 5. Wright, P.M., Seiple, I.B., and Myers, A.G. (2014). Angew. Chem. Int. Ed. 53, 8840–8869. 6. Bosch, F., and Rosich, L. (2008). Pharmacology 82, 171–179. 7. Lesch, J.E. (2007). The First Miracle Drugs: How the Sulfa Drugs Transformed Medicine (Oxford University Press). 8. Fischbach, M.A., and Walsh, C.T. (2009). Science 325, 1089–1093. 9. Kawaguchi, H., Naito, T., Nakagawa, S., and Fujisawa, K.-I. (1972). J. Antibiot. 25, 695–708. 10. Poehlsgaard, J., and Douthwaite, S. (2005). Nat. Rev. Microbiol. 3, 870–881. 11. Burke, M.D., and Schreiber, S.L. (2004). Angew. Chem. Int. Ed. 43, 46–58. 1School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chempr.2017.06.004
CATALYSIS
Reaction: Broad-Spectrum Antibiotics, a Call for Chemists Michelle F. Richter1 and Paul J. Hergenrother1,* Michelle F. Richter received her BS in biochemistry from Union College in 2011. She is now a National Science Foundation graduate fellow and member of the NIH Chemistry-Biology Interface Training Program in the
Hergenrother laboratory at the University of Illinois at Urbana-Champaign (UIUC), where she is working toward a PhD in chemistry. Paul J. Hergenrother received his BS in chemistry from the University of Notre Dame in 1994 and his PhD in chemistry at the University of Texas at Austin in 1999. After an American Cancer Society postdoctoral fellowship in the laboratory of Prof. Stuart Schreiber at Harvard University, in 2001 he joined the faculty at UIUC, where he is now the Kenneth L. Rinehart Jr. Endowed Chair in Natural Products Chemistry. In this issue of Chem, Micha Fridman discusses the central role of chemistry in future antibiotic discovery, and we strongly endorse Fridman’s thoughts about the importance of chemical synthesis in combating multidrugresistant (MDR) bacteria. It will be increasingly critical that this synthetic chemistry power be properly channeled, most notably to fight the growing problem of drug-resistant Gram-negative infections; as we argue below, the nature of this problem is especially suited to the skills of synthetic chemists. Discovering antibiotics effective against Gram-negative pathogens is challenging, largely because of the impermeable nature of the Gram-negative outer membrane. No new class of antibacterials with Gram-negative activity has been introduced into the clinic since the fluoroquinolones in 1968. As such, new drugs to combat the inevitable drug resistance of Gram-negatives have been developed only through modification of existing drugs, but such compounds are unlikely to provide the sustainable benefit afforded by an entirely new antibacterial class. Unfortunately, this situation is not improving, given that only one new class in clinical trials has antibacterial activity against Gram-negative pathogens; by comparison, there
are ten new classes in clinical trials for Gram-positive pathogens (http:// www.pewtrusts.org/en/multimedia/datavisualizations/2014/antibiotics-currentlyin-clinical-development). This dry pipeline for novel antibiotics renders MDR Gram-negative infections particularly concerning, as highlighted by the World Health Organization’s list of ‘‘Priority Pathogens’’ (issued in February 2017), for which new antibiotics are urgently needed. The list categorizes pathogens by threat level: critical, high, and medium priority. Nine out of the 12 pathogens listed, including all three critical priority pathogens (carbapenem-resistant Enterobacteriaceae [CRE], A. baumannii [AB], and P. aeruginosa [PA]), are Gram-negative bacteria. Efforts to discover natural products have for decades yielded new Grampositive-only antibiotics that have been developed into drugs, and this trend has continued with the relatively recent FDA approvals of daptomycin (in 2003), retapamulin (in 2007), and fidaxomicin (in 2011). In contrast, fewer broad-spectrum antibiotic classes have been identified through the screening of natural products. This is in part due to the outer membrane of Gram-negative bacteria, which restricts the diffusion of most small molecules, making compound accumulation inside Gram-negative bacteria markedly less likely than in Gram-positives. However, it is possible that other factors are at play as well. Of the four major antibacterial classes that have clinical coverage against all major Gram-negative pathogens (aminoglycosides, sulfa drugs, fluoroquinolones, and chemically modified b-lactams), three of them are synthetic. Why is this? We recently showed that compounds are most likely to accumulate in E. coli if they contain a sterically unencumbered amine (such as a primary amine), are relatively rigid, and have low globularity.1 It is possible that
compounds with primary amines are less likely to be isolated from natural sources by standard extraction and purification protocols. Or, it could be that the biosyntheses of such compounds are more challenging and costly to the producing organism or that there simply has not been the same selective pressure within bacterial niches for the evolution of dozens of different classes of broad-spectrum antibiotics. Whatever the reason, this dearth of broad-spectrum natural products presents a golden opportunity for chemists. The strategic application of synthetic chemistry will be key to keeping CRE, AB, and PA infections at bay, and there are at least two areas where chemists can make immediate contributions. First, our predictive guidelines suggest that certain Gram-positiveonly antibiotics can be converted to broad-spectrum agents, and the simplest method is to start with a compound imbued with the proper shape parameters (rigidity and globularity) and append a primary amine. This concept was demonstrated by the conversion of the Gram-positive-only natural product deoxynybomycin into 6DNM-NH3, a compound with broadspectrum activity, and our results also explain other serendipitous conversions, such as penicillin (a Grampositive-only antibiotic) to ampicillin (a broad-spectrum antibiotic).1 According to this same logic, dozens of outstanding Gram-positive-only antibiotics are ripe for conversion; these efforts will require careful analysis of structure-activity relationships and subsequent chemical synthesis to strategically place the amine at a position that does not impede interaction with the biological target. Impressive and robust syntheses for the tetracycline,2 macrolide,3 and mutilin4 classes of antibiotics show the power of bottom-up synthetic approaches in the construction of targeted antibiotic derivatives.
Chem 3, 8–14, July 13, 2017
11
have a primary amine; Figure 1A) goes a long way toward explaining the failures of compound screening to identify Gram-negative active antibiotics. As a complement to traditional methods, applying new synthetic methodologies to readily add amines to complex and rigid ring systems, including C–H activation strategies for installing an azide,7 cyano,8 alcohol,9 or halogen,10 will be critical to the development of compound collections biased toward the discovery of Gramnegative antibacterials.
Figure 1. The Dramatically Different Prevalence of Primary Amines in Screening Collections and Drugs (A) Analysis of the Chembridge MicroFormat Library (149,997 compounds) and a world drug database (4,309 compounds) shows that primary amines are almost 80 times less common in standard screening collections than in drugs (0.1% versus 7.8%). (B) Examples of drugs with primary amines; they are used for a variety of indications. (C) Primary amines in drugs are mostly present on primary and secondary carbons, showing that unhindered amines are common in drugs. A world drug database was analyzed with the assistance of Prof. Jo´ n Njarðarson (University of Arizona) through a search for all compounds that contained a nitrogen atom attached to a carbon and two hydrogens. The resulting compounds were then manually sorted to include only amines attached to an sp 3 -hybridized carbon.
Second, the predictive guidelines suggest a pathway for the creation of collections of compounds that are biased toward accumulation in Gram-negative bacteria. The notion that compounds in standard screening collections are unable to traverse the Gram-negative membranes and accumulate inside these bacteria has been suspected for some time,5 consistent with the notable failures of large compound screens to return any Gram-negative actives.6 Importantly, as mentioned above, many of the widely used broad-spectrum antibiotics are synthetic compounds; thus, the lesson here is certainly not to abandon synthetic compounds as a source of new broad-spectrum antibiotics. Rather, it is now clear from the predictive guidelines that simply making more compounds will
12
Chem 3, 8–14, July 13, 2017
not be sufficient for discovering new Gram-negative-active drugs. Instead, intelligent construction of compound collections will be essential so that these failures of the past are not repeated. Compounds in screening collections often have elevated numbers of rotatable bonds because of the ease of sp2-sp2 carbon-carbon coupling reactions, so to create bias toward broad-spectrum activity, synthetic strategies focused on the rapid construction of more rigid structures with contiguous and/or overlapping ring systems will be needed. Also, the addition of unhindered amines to compounds in screening collections is clearly an area of need. The fact that primary amines are largely absent from commercial screening libraries (0.1% of compounds in screening collections
Primary amines are probably absent from screening collections as a result of synthesis and purification challenges, as well as concerns about metabolism if the amine were to make it into a drug. However, it is important to note that the primary amine functional group is frequently present in approved drugs, including widely used medicines Januvia, Adderall, Tamiflu, L-Dopa, Lyrica, Vyvanse, Mematine, Valtrex, and Synthroid, as well as antibiotics such as ampicillin and vancomycin. In fact, our analysis shows that almost 8% of all drugs contain a primary amine, and these drugs are used for a variety of indications (some examples are shown in Figure 1B). The majority of these amines are attached to primary and secondary carbons (Figure 1C), showing that sterically unencumbered amine-containing compounds can indeed make outstanding drugs. The continued development of facile methods of synthesizing and purifying large numbers of compounds that meet the predictive guidelines will be critical, and we are optimistic that the implementation of modern synthetic tools and thinking will result in the discovery of much needed new classes of broad-spectrum antibiotics.
ACKNOWLEDGMENTS The University of Illinois has filed patents on compounds related to this work.
1. Richter, M.F., Drown, B.S., Riley, A.P., Garcia, A., Shirai, T., Svec, R.L., and Hergenrother, P.J. (2017). Nature 545, 299–304. 2. Charest, M.G., Lerner, C.D., Brubaker, J.D., Siegel, D.R., and Myers, A.G. (2005). Science 308, 395–398. 3. Seiple, I.B., Zhang, Z., Jakubec, P., LangloisMercier, A., Wright, P.M., Hog, D.T., Yabu, K., Allu, S.R., Fukuzaki, T., Carlsen, P.N., et al. (2016). Nature 533, 338–345. 4. Murphy, S.K., Zeng, M., and Herzon, S.B. (2017). Science 356, 956–959. 5. Silver, L.L. (2011). Clin. Microbiol. Rev. 24, 71–109. 6. Payne, D.J., Gwynn, M.N., Holmes, D.J., and Pompliano, D.L. (2007). Nat. Rev. Drug Discov. 6, 29–40. 7. Sharma, A., and Hartwig, J.F. (2015). Nature 517, 600–604. 8. McManus, J.B., and Nicewicz, D.A. (2017). J. Am. Chem. Soc. 139, 2880–2883. 9. Chen, M.S., and White, M.C. (2007). Science 318, 783–787. 10. Schmidt, V.A., Quinn, R.K., Brusoe, A.T., and Alexanian, E.J. (2014). J. Am. Chem. Soc. 136, 14389–14392. 1Department
of Chemistry, University of Illinois, Urbana, IL 61801, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chempr.2017.06.014
CATALYSIS
Reaction: Molecular Modeling for Novel Antibacterials Denis Fourches1,* Denis Fourches, PhD, is a molecular modeler and expert in cheminformatics in the Department of Chemistry and the Bioinformatics Research Center at North Carolina State University. His research focuses on the development and applications of novel predictive cheminformatics methods. I read the Catalysis piece by Dr. Micha Fridman with great interest. The burden of drug-resistant pathogens is already affecting healthcare systems to a great extent and will continue to do so if the research community at large cannot suc-
ceed in developing and delivering new antibacterial agents in the near future. Dr. Fridman properly underlines the need to develop new organic synthetic routes for complex molecules, especially the derivatives of natural products. Because their chemical synthesis is long (frequently more than 20 steps) and usually associated with low yields, such synthetic efforts become rapidly impractical and thus drastically limit the development and in-depth study of large series of congeneric analogs. Meanwhile, these series are highly useful for medicinal chemists to establish structure-activity relationships and enable the rational design of new molecules with enhanced potency and/or selectivity toward a particular pathogen. Herein, I would like to emphasize how cheminformatic and molecularmodeling approaches should be considered key methods and tools for achieving the overarching goal of developing the next generation of antibacterials. Developed over the past 30 years and benefiting from both the increase in computational power and the skyrocketing availability of chemogenomic data, these computational chemistry methods have become an essential element in the drug-discovery pipeline. Several well-known marketed drugs (e.g., imatinib, zanamivir, and nelfinavir) and countless drug candidates currently in clinical trials have been discovered and/or optimized by computational chemistry techniques. Essentially, these techniques allow for the rapid and inexpensive analysis, visualization, modeling, and in silico screening of virtual libraries containing either tens of millions of diverse molecules or smaller focused sets of congeneric series centered on known actives (e.g., fluoroquinolones and macrolides). In my opinion, two main categories of computational approaches are of strategic importance in the race toward new antimicrobials. Often, the main biological target of antibiotics is unknown, unavailable,
or very dissimilar to all other known structures from the Protein Data Bank (PDB). For all such cases, ligandbased modeling methods are relevant. Such techniques rely solely on the 2D and/or 3D molecular structures of the compounds included in the screening library without taking into account any structural information relative to the target protein. Recent improvements and successful case studies have involved (1) 3D pharmacophore modeling, which superimposes the conformations of a set of ligands and attempts to identify the key pharmacophoric features (e.g., aromatic ring, hydrophobic substituent, and H-bond donor) present in all actives but absent in inactives; (2) clustering algorithms that group compounds with high structural and/or conformational similarity into small clusters, allowing for the identification of activity cliffs (i.e., extremely similar compounds with dissimilar experimental activity) and local structure-activity relationships of high interest for rational drug design; and (3) quantitative structure-activity relationships (QSARs),1 which use 2D and 3D molecular descriptors and machine-learning techniques to establish quantified links between the structural features of ligands and their experimental activity (e.g., pKi, half maximal inhibitory concentration, minimum inhibitory concentration, and efflux).2 Importantly, QSAR modeling techniques have benefitted highly from the rapid development of artificial intelligence relying on modern learning algorithms (e.g., deep-learning neural networks, random forests, and support vector machines) and complex hierarchical architectures. When the 3D structure of the biological target is known (either experimentally determined by X-ray or nuclear magnetic resonance or computationally derived by homology modeling), additional structure-based modeling techniques can be considered. The most common is 3D molecular docking,
Chem 3, 8–14, July 13, 2017 ª 2017 Elsevier Inc.
13
10
enable a facile drug lead-optimization process, skeletons generated by the DOS approach should contain functional groups that enable derivation by the attachment of substituents in a site- and chemo-selective manner. By granting efficient access to unexplored regions of chemical space, the concept of DOS, fueled by creative ideas of organic chemists worldwide, is likely to continue to play an important role in re-enriching the pipeline with new antimicrobial drugs. To conclude, the complexity of the task of regenerating the currently sparse pipeline of antimicrobial drugs has put the development of synthetic methodologies for antimicrobial drug R&D under the spotlight given that the current synthetic methodologies are not at the point of perfection. Chemical research must focus on devising new and improved methodologies with an emphasis on synthetic efficiency, expanding the chemical spaces searched, and ensuring a feasible process for industrial-scale production of the new antimicrobial drugs that emerge from the pipeline. Although outstanding progress has been made in organic chemistry during the last century, the field is very far from the point at which it can rest on its laurels. Chemists should aspire to construct diverse molecular scaffolds of all levels of structural complexity from basic and inexpensive starting materials through a series of chemical transformations that provide full control over enantio-, regio-, and chemo-selectivity. This goal will be achieved through creativity, improved synthetic methodologies, and importantly, a focus on the development of novel reactions for the formation and cleavage of chemical bonds. With an increase in funding and research focus in the near future, the development of novel synthetic tools in combination with the identification and structural characterization of novel microbial drug targets will undoubtedly put antimicrobial drug R&D back on the right
Chem 3, 8–14, July 13, 2017 ª 2017 Published by Elsevier Inc.
track and enable mankind to gain the upper hand in combating microbial infections in the future. 1. Armelagos, G.J., Brown, P.J., and Turner, B. (2005). Soc. Sci. Med. 61, 755–765. 2. Laxminarayan, R., Duse, A., Wattal, C., Zaidi, A.K., Wertheim, H.F., Sumpradit, N., Vlieghe, E., Hara, G.L., Gould, I.M., Goossens, H., et al. (2013). Lancet Infect. Dis. 13, 1057–1098. 3. Davies, J., and Davies, D. (2010). Microbiol. Mol. Biol. Rev. 74, 417–433. 4. Goff, D.A., Kullar, R., Goldstein, E.J.C., Gilchrist, M., Nathwani, D., Cheng, A.C., Cairns, K.A., Escando´n-Vargas, K., Villegas, M.V., Brink, A., et al. (2017). Lancet Infect. Dis. 17, e56–e63. 5. Wright, P.M., Seiple, I.B., and Myers, A.G. (2014). Angew. Chem. Int. Ed. 53, 8840–8869. 6. Bosch, F., and Rosich, L. (2008). Pharmacology 82, 171–179. 7. Lesch, J.E. (2007). The First Miracle Drugs: How the Sulfa Drugs Transformed Medicine (Oxford University Press). 8. Fischbach, M.A., and Walsh, C.T. (2009). Science 325, 1089–1093. 9. Kawaguchi, H., Naito, T., Nakagawa, S., and Fujisawa, K.-I. (1972). J. Antibiot. 25, 695–708. 10. Poehlsgaard, J., and Douthwaite, S. (2005). Nat. Rev. Microbiol. 3, 870–881. 11. Burke, M.D., and Schreiber, S.L. (2004). Angew. Chem. Int. Ed. 43, 46–58. 1School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chempr.2017.06.004
CATALYSIS
Reaction: Broad-Spectrum Antibiotics, a Call for Chemists Michelle F. Richter1 and Paul J. Hergenrother1,* Michelle F. Richter received her BS in biochemistry from Union College in 2011. She is now a National Science Foundation graduate fellow and member of the NIH Chemistry-Biology Interface Training Program in the
Hergenrother laboratory at the University of Illinois at Urbana-Champaign (UIUC), where she is working toward a PhD in chemistry. Paul J. Hergenrother received his BS in chemistry from the University of Notre Dame in 1994 and his PhD in chemistry at the University of Texas at Austin in 1999. After an American Cancer Society postdoctoral fellowship in the laboratory of Prof. Stuart Schreiber at Harvard University, in 2001 he joined the faculty at UIUC, where he is now the Kenneth L. Rinehart Jr. Endowed Chair in Natural Products Chemistry. In this issue of Chem, Micha Fridman discusses the central role of chemistry in future antibiotic discovery, and we strongly endorse Fridman’s thoughts about the importance of chemical synthesis in combating multidrugresistant (MDR) bacteria. It will be increasingly critical that this synthetic chemistry power be properly channeled, most notably to fight the growing problem of drug-resistant Gram-negative infections; as we argue below, the nature of this problem is especially suited to the skills of synthetic chemists. Discovering antibiotics effective against Gram-negative pathogens is challenging, largely because of the impermeable nature of the Gram-negative outer membrane. No new class of antibacterials with Gram-negative activity has been introduced into the clinic since the fluoroquinolones in 1968. As such, new drugs to combat the inevitable drug resistance of Gram-negatives have been developed only through modification of existing drugs, but such compounds are unlikely to provide the sustainable benefit afforded by an entirely new antibacterial class. Unfortunately, this situation is not improving, given that only one new class in clinical trials has antibacterial activity against Gram-negative pathogens; by comparison, there
are ten new classes in clinical trials for Gram-positive pathogens (http:// www.pewtrusts.org/en/multimedia/datavisualizations/2014/antibiotics-currentlyin-clinical-development). This dry pipeline for novel antibiotics renders MDR Gram-negative infections particularly concerning, as highlighted by the World Health Organization’s list of ‘‘Priority Pathogens’’ (issued in February 2017), for which new antibiotics are urgently needed. The list categorizes pathogens by threat level: critical, high, and medium priority. Nine out of the 12 pathogens listed, including all three critical priority pathogens (carbapenem-resistant Enterobacteriaceae [CRE], A. baumannii [AB], and P. aeruginosa [PA]), are Gram-negative bacteria. Efforts to discover natural products have for decades yielded new Grampositive-only antibiotics that have been developed into drugs, and this trend has continued with the relatively recent FDA approvals of daptomycin (in 2003), retapamulin (in 2007), and fidaxomicin (in 2011). In contrast, fewer broad-spectrum antibiotic classes have been identified through the screening of natural products. This is in part due to the outer membrane of Gram-negative bacteria, which restricts the diffusion of most small molecules, making compound accumulation inside Gram-negative bacteria markedly less likely than in Gram-positives. However, it is possible that other factors are at play as well. Of the four major antibacterial classes that have clinical coverage against all major Gram-negative pathogens (aminoglycosides, sulfa drugs, fluoroquinolones, and chemically modified b-lactams), three of them are synthetic. Why is this? We recently showed that compounds are most likely to accumulate in E. coli if they contain a sterically unencumbered amine (such as a primary amine), are relatively rigid, and have low globularity.1 It is possible that
compounds with primary amines are less likely to be isolated from natural sources by standard extraction and purification protocols. Or, it could be that the biosyntheses of such compounds are more challenging and costly to the producing organism or that there simply has not been the same selective pressure within bacterial niches for the evolution of dozens of different classes of broad-spectrum antibiotics. Whatever the reason, this dearth of broad-spectrum natural products presents a golden opportunity for chemists. The strategic application of synthetic chemistry will be key to keeping CRE, AB, and PA infections at bay, and there are at least two areas where chemists can make immediate contributions. First, our predictive guidelines suggest that certain Gram-positiveonly antibiotics can be converted to broad-spectrum agents, and the simplest method is to start with a compound imbued with the proper shape parameters (rigidity and globularity) and append a primary amine. This concept was demonstrated by the conversion of the Gram-positive-only natural product deoxynybomycin into 6DNM-NH3, a compound with broadspectrum activity, and our results also explain other serendipitous conversions, such as penicillin (a Grampositive-only antibiotic) to ampicillin (a broad-spectrum antibiotic).1 According to this same logic, dozens of outstanding Gram-positive-only antibiotics are ripe for conversion; these efforts will require careful analysis of structure-activity relationships and subsequent chemical synthesis to strategically place the amine at a position that does not impede interaction with the biological target. Impressive and robust syntheses for the tetracycline,2 macrolide,3 and mutilin4 classes of antibiotics show the power of bottom-up synthetic approaches in the construction of targeted antibiotic derivatives.
Chem 3, 8–14, July 13, 2017
11
have a primary amine; Figure 1A) goes a long way toward explaining the failures of compound screening to identify Gram-negative active antibiotics. As a complement to traditional methods, applying new synthetic methodologies to readily add amines to complex and rigid ring systems, including C–H activation strategies for installing an azide,7 cyano,8 alcohol,9 or halogen,10 will be critical to the development of compound collections biased toward the discovery of Gramnegative antibacterials.
Figure 1. The Dramatically Different Prevalence of Primary Amines in Screening Collections and Drugs (A) Analysis of the Chembridge MicroFormat Library (149,997 compounds) and a world drug database (4,309 compounds) shows that primary amines are almost 80 times less common in standard screening collections than in drugs (0.1% versus 7.8%). (B) Examples of drugs with primary amines; they are used for a variety of indications. (C) Primary amines in drugs are mostly present on primary and secondary carbons, showing that unhindered amines are common in drugs. A world drug database was analyzed with the assistance of Prof. Jo´ n Njarðarson (University of Arizona) through a search for all compounds that contained a nitrogen atom attached to a carbon and two hydrogens. The resulting compounds were then manually sorted to include only amines attached to an sp 3 -hybridized carbon.
Second, the predictive guidelines suggest a pathway for the creation of collections of compounds that are biased toward accumulation in Gram-negative bacteria. The notion that compounds in standard screening collections are unable to traverse the Gram-negative membranes and accumulate inside these bacteria has been suspected for some time,5 consistent with the notable failures of large compound screens to return any Gram-negative actives.6 Importantly, as mentioned above, many of the widely used broad-spectrum antibiotics are synthetic compounds; thus, the lesson here is certainly not to abandon synthetic compounds as a source of new broad-spectrum antibiotics. Rather, it is now clear from the predictive guidelines that simply making more compounds will
12
Chem 3, 8–14, July 13, 2017
not be sufficient for discovering new Gram-negative-active drugs. Instead, intelligent construction of compound collections will be essential so that these failures of the past are not repeated. Compounds in screening collections often have elevated numbers of rotatable bonds because of the ease of sp2-sp2 carbon-carbon coupling reactions, so to create bias toward broad-spectrum activity, synthetic strategies focused on the rapid construction of more rigid structures with contiguous and/or overlapping ring systems will be needed. Also, the addition of unhindered amines to compounds in screening collections is clearly an area of need. The fact that primary amines are largely absent from commercial screening libraries (0.1% of compounds in screening collections
Primary amines are probably absent from screening collections as a result of synthesis and purification challenges, as well as concerns about metabolism if the amine were to make it into a drug. However, it is important to note that the primary amine functional group is frequently present in approved drugs, including widely used medicines Januvia, Adderall, Tamiflu, L-Dopa, Lyrica, Vyvanse, Mematine, Valtrex, and Synthroid, as well as antibiotics such as ampicillin and vancomycin. In fact, our analysis shows that almost 8% of all drugs contain a primary amine, and these drugs are used for a variety of indications (some examples are shown in Figure 1B). The majority of these amines are attached to primary and secondary carbons (Figure 1C), showing that sterically unencumbered amine-containing compounds can indeed make outstanding drugs. The continued development of facile methods of synthesizing and purifying large numbers of compounds that meet the predictive guidelines will be critical, and we are optimistic that the implementation of modern synthetic tools and thinking will result in the discovery of much needed new classes of broad-spectrum antibiotics.
ACKNOWLEDGMENTS The University of Illinois has filed patents on compounds related to this work.
1. Richter, M.F., Drown, B.S., Riley, A.P., Garcia, A., Shirai, T., Svec, R.L., and Hergenrother, P.J. (2017). Nature 545, 299–304. 2. Charest, M.G., Lerner, C.D., Brubaker, J.D., Siegel, D.R., and Myers, A.G. (2005). Science 308, 395–398. 3. Seiple, I.B., Zhang, Z., Jakubec, P., LangloisMercier, A., Wright, P.M., Hog, D.T., Yabu, K., Allu, S.R., Fukuzaki, T., Carlsen, P.N., et al. (2016). Nature 533, 338–345. 4. Murphy, S.K., Zeng, M., and Herzon, S.B. (2017). Science 356, 956–959. 5. Silver, L.L. (2011). Clin. Microbiol. Rev. 24, 71–109. 6. Payne, D.J., Gwynn, M.N., Holmes, D.J., and Pompliano, D.L. (2007). Nat. Rev. Drug Discov. 6, 29–40. 7. Sharma, A., and Hartwig, J.F. (2015). Nature 517, 600–604. 8. McManus, J.B., and Nicewicz, D.A. (2017). J. Am. Chem. Soc. 139, 2880–2883. 9. Chen, M.S., and White, M.C. (2007). Science 318, 783–787. 10. Schmidt, V.A., Quinn, R.K., Brusoe, A.T., and Alexanian, E.J. (2014). J. Am. Chem. Soc. 136, 14389–14392. 1Department
of Chemistry, University of Illinois, Urbana, IL 61801, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chempr.2017.06.014
CATALYSIS
Reaction: Molecular Modeling for Novel Antibacterials Denis Fourches1,* Denis Fourches, PhD, is a molecular modeler and expert in cheminformatics in the Department of Chemistry and the Bioinformatics Research Center at North Carolina State University. His research focuses on the development and applications of novel predictive cheminformatics methods. I read the Catalysis piece by Dr. Micha Fridman with great interest. The burden of drug-resistant pathogens is already affecting healthcare systems to a great extent and will continue to do so if the research community at large cannot suc-
ceed in developing and delivering new antibacterial agents in the near future. Dr. Fridman properly underlines the need to develop new organic synthetic routes for complex molecules, especially the derivatives of natural products. Because their chemical synthesis is long (frequently more than 20 steps) and usually associated with low yields, such synthetic efforts become rapidly impractical and thus drastically limit the development and in-depth study of large series of congeneric analogs. Meanwhile, these series are highly useful for medicinal chemists to establish structure-activity relationships and enable the rational design of new molecules with enhanced potency and/or selectivity toward a particular pathogen. Herein, I would like to emphasize how cheminformatic and molecularmodeling approaches should be considered key methods and tools for achieving the overarching goal of developing the next generation of antibacterials. Developed over the past 30 years and benefiting from both the increase in computational power and the skyrocketing availability of chemogenomic data, these computational chemistry methods have become an essential element in the drug-discovery pipeline. Several well-known marketed drugs (e.g., imatinib, zanamivir, and nelfinavir) and countless drug candidates currently in clinical trials have been discovered and/or optimized by computational chemistry techniques. Essentially, these techniques allow for the rapid and inexpensive analysis, visualization, modeling, and in silico screening of virtual libraries containing either tens of millions of diverse molecules or smaller focused sets of congeneric series centered on known actives (e.g., fluoroquinolones and macrolides). In my opinion, two main categories of computational approaches are of strategic importance in the race toward new antimicrobials. Often, the main biological target of antibiotics is unknown, unavailable,
or very dissimilar to all other known structures from the Protein Data Bank (PDB). For all such cases, ligandbased modeling methods are relevant. Such techniques rely solely on the 2D and/or 3D molecular structures of the compounds included in the screening library without taking into account any structural information relative to the target protein. Recent improvements and successful case studies have involved (1) 3D pharmacophore modeling, which superimposes the conformations of a set of ligands and attempts to identify the key pharmacophoric features (e.g., aromatic ring, hydrophobic substituent, and H-bond donor) present in all actives but absent in inactives; (2) clustering algorithms that group compounds with high structural and/or conformational similarity into small clusters, allowing for the identification of activity cliffs (i.e., extremely similar compounds with dissimilar experimental activity) and local structure-activity relationships of high interest for rational drug design; and (3) quantitative structure-activity relationships (QSARs),1 which use 2D and 3D molecular descriptors and machine-learning techniques to establish quantified links between the structural features of ligands and their experimental activity (e.g., pKi, half maximal inhibitory concentration, minimum inhibitory concentration, and efflux).2 Importantly, QSAR modeling techniques have benefitted highly from the rapid development of artificial intelligence relying on modern learning algorithms (e.g., deep-learning neural networks, random forests, and support vector machines) and complex hierarchical architectures. When the 3D structure of the biological target is known (either experimentally determined by X-ray or nuclear magnetic resonance or computationally derived by homology modeling), additional structure-based modeling techniques can be considered. The most common is 3D molecular docking,
Chem 3, 8–14, July 13, 2017 ª 2017 Elsevier Inc.
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