Paul A Wender1, Ryan V Quiroz1, Matthew C Stevens1. 1. Departments of Chemistry and Chemical and Systems Biology, Stanford University, Stanford, California 94305-5080, United States.
Abstract
In 1996, a snapshot of the field of synthesis was provided by many of its thought leaders in a Chemical Reviews thematic issue on "Frontiers in Organic Synthesis". This Accounts of Chemical Research thematic issue on "Synthesis, Design, and Molecular Function" is intended to provide further perspective now from well into the 21st century. Much has happened in the past few decades. The targets, methods, strategies, reagents, procedures, goals, funding, practices, and practitioners of synthesis have changed, some in dramatic ways as documented in impressive contributions to this issue. However, a constant for most synthesis studies continues to be the goal of achieving function with synthetic economy. Whether in the form of new catalysts, reagents, therapeutic leads, diagnostics, drug delivery systems, imaging agents, sensors, materials, energy generation and storage systems, bioremediation strategies, or molecules that challenge old theories or test new ones, the function of a target has been and continues to be a major and compelling justification for its synthesis. While the targets of synthesis have historically been heavily represented by natural products, increasingly design, often inspired by natural structures, is providing a new source of target structures exhibiting new or natural functions and new or natural synthetic challenges. Complementing isolation and screening approaches to new target identification, design enables one to create targets de novo with an emphasis on sought-after function and synthetic innovation with step-economy. Design provides choice. It allows one to determine how close a synthesis will come to the ideal synthesis and how close a structure will come to the ideal function. In this Account, we address studies in our laboratory on function-oriented synthesis (FOS), a strategy to achieve function by design and with synthetic economy. By starting with function rather than structure, FOS places an initial emphasis on target design, thereby harnessing the power of chemists and computers to create new structures with desired functions that could be prepared in a simple, safe, economical, and green, if not ideal, fashion. Reported herein are examples of FOS associated with (a) molecular recognition, leading to the first designed phorbol-inspired protein kinase C regulatory ligands, the first designed bryostatin analogs, the newest bryologs, and a new family of designed kinase inhibitors, (b) target modification, leading to highly simplified but functionally competent photonucleases-molecules that cleave DNA upon photoactivation, (c) drug delivery, leading to cell penetrating molecular transporters, molecules that ferry other attached or complexed molecules across biological barriers, and (d) new reactivity-regenerating reagents in the form of functional equivalents of butatrienes, reagents that allow for back-to-back three-component cycloaddition reactions, thus achieving structural complexity and value with step-economy. While retrosynthetic analysis seeks to identify the best way to make a target, retrofunction analysis seeks to identify the best targets to make. In essence, form (structure) follows function.
In 1996, a snapshot of the field of synthesis was provided by many of its thought leaders in a Chemical Reviews thematic issue on "Frontiers in Organic Synthesis". This Accounts of Chemical Research thematic issue on "Synthesis, Design, and Molecular Function" is intended to provide further perspective now from well into the 21st century. Much has happened in the past few decades. The targets, methods, strategies, reagents, procedures, goals, funding, practices, and practitioners of synthesis have changed, some in dramatic ways as documented in impressive contributions to this issue. However, a constant for most synthesis studies continues to be the goal of achieving function with synthetic economy. Whether in the form of new catalysts, reagents, therapeutic leads, diagnostics, drug delivery systems, imaging agents, sensors, materials, energy generation and storage systems, bioremediation strategies, or molecules that challenge old theories or test new ones, the function of a target has been and continues to be a major and compelling justification for its synthesis. While the targets of synthesis have historically been heavily represented by natural products, increasingly design, often inspired by natural structures, is providing a new source of target structures exhibiting new or natural functions and new or natural synthetic challenges. Complementing isolation and screening approaches to new target identification, design enables one to create targets de novo with an emphasis on sought-after function and synthetic innovation with step-economy. Design provides choice. It allows one to determine how close a synthesis will come to the ideal synthesis and how close a structure will come to the ideal function. In this Account, we address studies in our laboratory on function-oriented synthesis (FOS), a strategy to achieve function by design and with synthetic economy. By starting with function rather than structure, FOS places an initial emphasis on target design, thereby harnessing the power of chemists and computers to create new structures with desired functions that could be prepared in a simple, safe, economical, and green, if not ideal, fashion. Reported herein are examples of FOS associated with (a) molecular recognition, leading to the first designed phorbol-inspired protein kinase C regulatory ligands, the first designed bryostatin analogs, the newest bryologs, and a new family of designed kinase inhibitors, (b) target modification, leading to highly simplified but functionally competent photonucleases-molecules that cleave DNA upon photoactivation, (c) drug delivery, leading to cell penetrating molecular transporters, molecules that ferry other attached or complexed molecules across biological barriers, and (d) new reactivity-regenerating reagents in the form of functional equivalents of butatrienes, reagents that allow for back-to-back three-component cycloaddition reactions, thus achieving structural complexity and value with step-economy. While retrosynthetic analysis seeks to identify the best way to make a target, retrofunction analysis seeks to identify the best targets to make. In essence, form (structure) follows function.
The extraordinary and to some extent
inexplicable production of
urea without the assistance of vital functions, for which we are indebted
to Wöhler, must be considered one of the discoveries with which
a new era in science has commenced.That new era has since transformed
science with consequences of
immense societal benefit. From new medicines to materials and extraordinary
research tools, our ability to make and manipulate molecules has profoundly
advanced our understanding of molecular structure, reactivity, and
function and with that contributed to the molecularization of science
from molecular anthropology to zoology and most disciplines in between.[2] Over a period of less than 200 years, the synthesis
of natural products, once considered impossible, has become increasingly
common, increasingly impressive, and increasingly consequential to
research, our economy, our health care, and our standard of living.In 1996, a snapshot of the field of synthesis was provided by many
of its thought leaders.[3] This Accounts
of Chemical Research thematic issue on “Synthesis,
Design, and Molecular Function” provides an inspiring sequel
now with a 21st century perspective. Our own contribution addresses
studies in our laboratory on function-oriented synthesis (FOS), a strategy for achieving function with synthetic economy,
a goal of most “orientations” in synthesis.[4] By starting with function rather than structure,
FOS places an initial emphasis on target design, thereby harnessing
the power of chemists and computers to create new structures with
natural or new functions that could be prepared in a simple, safe,
economical, and green if not ideal fashion.[5] While retrosynthetic analysis seeks to identify the best way to
make a target, retrofunction analysis seeks to identify the best targets
to make. In essence, form (structure) follows function.Whether
natural or designed, the targets of organic synthesis have
increased in number and diversity over the years from simple to complex
molecules and even molecular systems. As impressively chronicled by
Cragg, Grothaus, and Newman,[6] the sources
of new chemical entities (NCEs) over the last few decades have been
diverse. Natural products, historically structures of great synthetic
and medicinal interest, continue to figure as new therapeutic leads,
accounting for 6% of the 1024 NCEs reported between January 1981 and
October 2009. An additional 27% of the reported NCEs are derivatives
of natural products. Significantly, 30% of the NCEs are synthetic
compounds that share a functional or pharmacophoric relationship with
natural products, while 37% are synthetic compounds with no natural
product connection. These distributions are likely to fluctuate due
to funding decisions and the realization that many natural products,
while significant leads, are not optimized for their intended use
as, for example, therapeutic agents. Thus, while natural products
continue to inspire new synthetic strategies and methods based on
their structures, they increasingly also inspire the design of new
and more synthetically accessible structures based on their function
(activity). Because a given function can be achieved with many different
structures, design-for-function becomes a powerful strategy for creating
totally new targets inspired by natural product leads or by abiological
needs. β-Lactam antibiotic structures, as one example, changed
over time from natural to designed and often from complex to less
so, while their activity (function) was largely preserved or improved
(Figure 1).[7] A key
to this success was knowledge of their mechanism of action and its
use in designing simpler and thus more synthetically accessible targets
with similar or improved function. Pertinent to current discussions
about making molecules, fermentation, biosynthesis, semisynthesis,
synthetic biology, synthetic methodology, and abiological synthesis
all played prominent and often complementary roles in advancing this
field.
Figure 1
β-Lactam antibiotics: Similar function, different structures.
β-Lactam antibiotics: Similar function, different structures.What’s next? The answer
is complex and not driven only by
scientific curiosity since funding also influences direction. It is
however hard to imagine a time when natural products, representing
3.8 billion years of chemical experimentation and information, would
not figure as prominent sources of inspiration and value. At the same
time, given the structure generating and searching capabilities of
computers, it is equally hard to imagine that virtual structures and
libraries would not increasingly figure as sources of new structures
and inspiration. Think about it. How many of us have drawn or doodled
a new structure perhaps as a chiral ligand for asymmetric catalysis,
a reagent for synthesis or a probe to test a theory. Computers can
do this on a massive scale. The recent report of a 166 billion compound
library exemplifies this potentially game-changing source of new structures,
synthesis inspiration, and function.[8] Driven
by graph theory and guided by structural theory, this virtual approach
to structure generation can identify all possible connections of selected
atoms found, for example, in many known and as yet unknown drug leads.
It deselects potentially problematic features (e.g., strained bonds),
providing a virtual library that can be searched for structures of
interest (Figure 2). While a work in progress,
it is projected to reach a trillion compounds in the near future and
should vastly exceed that as its potential is further explored.
Figure 2
Generation
of a 166 billion compound virtual library. Modified
from Reymond et al.[8]
Generation
of a 166 billion compound virtual library. Modified
from Reymond et al.[8]Virtual structure generation has great but largely unexploited
value. It can be used to generate not only as yet undiscovered natural
products but also structures that exhibit atom connectivities not
encountered in biosynthetic pathways. While searching such a vast
library, say for pharmacophoric features,[9] is beyond human capabilities, it is as simple computationally as
doing a word search on Google. In collaboration with the Reymond Group,
for example, we have extracted a library of 90 000 hits from
a 166 billion compound library based on a search for structures with
a bryostatin- or phorbol-like pharmacophore (function). Many of these
hits are as inspiring synthetically, and potentially functionally,
as the natural products upon which the pharmacophores are based. Fundamentally,
this is not new, since any lecture on constitutional isomers has addressed
this approach “by hand” often in connection with identifying
all the constitutional isomers of, say, pentane. What is new is the
power of computers to do this exhaustively for larger collections
of atoms and to identify and characterize the expected properties
of the newly identified targets in terms of attributes of structural
and functional interest.Nature’s vast library and computer-derived
virtual libraries
can be expected to provide a continuing source of new structural challenges
to test existing reactions and strategies and to inspire the design
of new ones. If so, then what’s next?[2] Are there other sources of structures? Or in the words of Dieter
Seebach: “Organic Synthesis – Where Now?”[10] Answers to these questions will vary from individual
to individual. However, most would agree that the goals of synthesis
are increasingly related to not just target structure but target function.
It is indeed the function of a structure that is often used as justification
and motivation for its synthesis. In 2014, for example, ∼134
total syntheses were reported in ACS journals alone. The vast majority
of these efforts called attention, in varying degree, to the biological
activity of the targets. With over 7000 diseases for which we have
no effective therapy, it is likely that synthetic chemists will continue
to rise to meet these, as yet unmet, challenges associated with function.Structures with function can be discovered through screening of
natural and virtual libraries. A third source is through design. This
differs from natural and virtual approaches in that the structures
are created de novo to achieve function and ease
of synthesis. Such design-driven structure generation has lagged behind
discovery-driven screening in producing functional targets partly
because it requires an understanding of complex and dynamic molecular
systems. Increasingly, however, with the emergence of powerful analytical
and computational tools, such knowledge becomes more accessible and
design becomes a more promising path to creating new structures with
function. An attractive aspect of this approach is that design can
also be used to create new synthetic challenges and ensure a more
practical, step-economical, and “green” outcome.[5,11] Here we describe the genesis and an overview of representative FOS
studies in our laboratory with examples of FOS directed at molecular
recognition, reactive intermediate generation, drug delivery, and
reagent equivalency.Our FOS studies evolved from an early interest
in carcinogenesis.[12] The basis for that
interest was quite logical.
Cancer is a major killer. There are three ways to intervene in addressing
cancer or any disease: therapy, detection, and prevention. Of these,
prevention is the most effective and least costly. Prevention in turn
requires knowledge of how a disease starts. For cancer, it was clear
then that carcinogens play a role. What was less clear then and still
not fully understood now is the role of tumor promoters in carcinogenesis.
Tumor promoters are noncarcinogenic agents that amplify the effect
of a carcinogen. The most potent tumor promoters are the plant-derived
phorbol esters (PEs).[13] We thus set out
to make these agents and to study their role in carcinogenesis.Contemporaneously, Nishizuka reported a new family of proteins
now collectively known as protein kinase C (PKC).[14] It was found that PKC isoforms are regulated by the binding
of endogenous diacylglycerol (DAG). In what for us was a remarkable
confluence of events, it was subsequently found that mammalianDAG
competes with plant-derived PEs in binding to PKC. Thus, simple DAG
and the more complex PEs shared a similar function (binding to the
same site of PKC) but not a similar structure. Through extensive computer
analyses of the two structures, we identified pharmacophore candidates,
among which the best spatial correlation was between the oxygens at
C9, C20, and C4/C3 of PEs and a similar set of three hydrogen-bond
donor and acceptor oxygens in DAG. This provided a blueprint for the
design of PKC modulators and led to the first designed ligand (1) that bound to the regulatory domain of PKC competitively
with the PEs and DAG and elicited function (phosphorylation) (Figure 3).[12] While years later
we successfully completed the total synthesis of phorbol,[15] our designed and notably simpler agent was prepared
in only 2 weeks, providing function with step-economy by design.
Figure 3
PKC activators
(phorbol 13-acetate, PDB 1PTR):[16] Different
structures, similar pharmacophores and function.
PKC activators
(phorbol 13-acetate, PDB 1PTR):[16] Different
structures, similar pharmacophores and function.There were several lessons learned from this early study.
The function
of a molecule, in this case binding to PKC, can be emulated by only
a subset of its complex structure. Thus, the time required to design
and synthesize simpler systems can often be greatly reduced relative
to more complex systems, thereby favoring time-economy,[5] a priority goal in research and especially that
directed at clinical needs. Finally, the step-economy achieved through
synthesis-informed design can dramatically lower the cost of accessing
tool compounds or therapeutic leads. The success of this FOS strategy
is based on using natural products to inspire design, thereby speeding
access to their functions. It is noteworthy however that the designed
product is not a derivative of the natural product, that is, a structural analog, but rather a simplified functional analog incorporating only its pharmacophoric features. This difference
is sometimes lost in discussions about diverted total syntheses.[17] There are no diversions in design. One starts
with a functional goal and creates a structure to achieve it.The impact of this study was heightened by the report of Pettit[18] on another DAG competitive PKC binder, namely,
marine-derived bryostatin. Significantly, bryostatin, unlike PEs,
does not exhibit tumor promoter activity, exemplifying PKC’s
complex role in cellular function. PKC has since been connected to
many therapeutic indications including cancer,[19] Alzheimer’s disease,[20] and eradication of HIV/AIDS.[21] As the
story of bryostatin’s clinical potential took shape, concerns
about its availability grew. Bryostatin is thought to be produced
in a symbiotic relationship involving a bryozoan (Bugula neritina) and a bacterium (Endobugula sertula) in its gut.
Fourteen tons of the source organism was needed to produce only 18
g of bryostatin for clinical trials. While the potency of bryostatin
(dosed at ∼25–125 μg/m2) allowed for
many clinical studies, its timely supply remained an issue and therefore
became a superb test for FOS.Following the protocol successfully
used with DAG and PEs, computer
generated structures of bryostatin and DAG were compared to identify
shared pharmacophoric features.[22] The best
correlations suggested a hydrogen-bonding role for the C1, C26, and
C19 oxygens of bryostatin in PKC binding. However, unlike conformationally
restricted PEs, bryostatin can assume thousands of conformations,
many energetically close to the global minimum. As such, we took a
conservative approach to designing functional analogs. The entire
lower half of the bryostatin structure (largely the C-ring and C1
lactone), which included the putative pharmacophoric features and
thus the functionality contacting PKC, was kept intact while the A-
and B-rings were dramatically simplified and modified (C14 replaced
with an oxygen to enable a convergent synthesis). Synthesis of the
resultant simplified structure 2 required only ∼30
steps, while at the time, syntheses of natural bryostatins required
69–89 steps. Significantly, this study led to the synthesis
of the first designed bryostatin analog, which along with other “bryologs”
exhibited affinities to PKC comparable to or better than the natural
bryostatins (Figure 4).[23] Importantly, the best analogs at the time, dubbed nanolog
and picolog (2) based on their PKC affinities, performed
significantly better than bryostatin in inhibiting the growth of humancancer cells as determined in a study by the National Cancer Institute
(NIH).[23] These and related functional analogs
have since been advanced to animal studies and are in preclinical
evaluation for the treatment of Alzheimer’s disease and for
the eradication of HIV/AIDS. Some of this work and related FOS contributions
on bryostatin analogs from others have been reviewed recently.[23] For this analysis, the important take-home message
from our work is that computer-assisted design provided simplified
and thus more synthetically accessible functional analogs that perform
as well as or better than the natural product.
Figure 4
Function with step-economy
through design: PKC potency with progressive
simplification. The Ki values are for
PKCδ. *Ki values are for PKC rat
brain mix.
Function with step-economy
through design: PKC potency with progressive
simplification. The Ki values are for
PKCδ. *Ki values are for PKCrat
brain mix.Are further structural simplifications
possible? It follows from
our pharmacophore hypothesis that the A- and B-rings of bryostatin
contribute to PKC binding by preorganizing the pharmacophoric groups
in contact with the protein and as such are subject to further simplification.
Recently, we reported analogs in which these rings are replaced by
commercially available salicylic acid, a substitution that further
reduces step count (3, Figure 4).[24] Computer comparisons of the designed
analog with bryostatin showed an excellent spatial correlation of
recognition domain atoms (RMSD = 0.05 Å). In line with this analysis,
the lead salicylate-derived analog showed potent binding to PKC β
and δ with Ki’s of 3.1 and
1.9 nM, respectively, comparable to bryostatin with Ki’s of 1.0 and 1.1 nM. Requiring only ∼23
steps to make relative to the ∼40 steps required for the best
syntheses to date of natural bryostatins,[23] this recent FOS study provides step-economical access to potent
new PKC modulators.The aforementioned studies sought to understand
how complex molecules
like PEs and bryostatin mimic DAG in binding to PKC and from that
how to design simplified PE and bryostatin analogs. A series of deletions
and simplifying substitutions were employed. An unaddressed complementary
question is whether DAG, an already simplified, natural PKC regulator,
could be modified to create PE- or bryostatin-like activity. Interestingly,
DAG is significantly less potent than plant-derived PEs and marine-derived
bryostatin, suggesting that its greater flexibility (entropy) might
contribute to its lower PKC affinity. The FOS challenge thus becomes
one of designing a less flexible DAG. Early studies showed, however,
that modifications of DAG, including heteroatom substitution, changes
in the ester linkages, and insertion of additional atoms in the glycerol
backbone, result in compounds with lower PKC affinities. Thus, one
needs a way to restrict the DAG conformation without significant changes
to its structure. Our approach to this challenge led to the creation
of a new class of molecules, cyclic DAGs (cDAGs) (Figure 5).[25] By connecting the
lipid termini in DAG one creates a cDAG, a macrocyclic bis-lactone
(4). Like other macrolides this changes the population
of conformers without changing the functionality. Preliminary studies
show that cDAGs bind to PKC isoforms with affinities that vary expectedly
with ring size but approach values in the single digit nanomolar range
and differ from acyclic DAGs in PKC selectivity. Significantly, synthetic
access to cDAGs requires only 4 steps. Our cDAG analogs
compete with the original triad of PKC modulators, providing new,
more accessible, and potent leads for each scaffold. Our early and
ongoing FOS work on bryostatin and related compounds has now been
joined by others making noteworthy contributions to this field.[26]
Figure 5
Four steps to cyclic diacylglycerols (4),
a new family
of PKC modulators.
Four steps to cyclic diacylglycerols (4),
a new family
of PKC modulators.How general is this FOS
approach? Given the role of kinases in
human diseases, major research efforts have been directed at identifying
kinase inhibitors by screening natural and non-natural chemical libraries.
Several years ago, we launched a FOS program directed at designing
kinase inhibitors that would bind to the kinase ATP-binding site and
thus block function. Our starting point was, not unlike in the above
studies, a natural product, staurosporine. Staurosporine is a promiscuous
kinase inhibitor, affecting >253 kinases with Kd’s in the micro- to nanomolar range.[27] Our goal here was to first achieve binding using
readily
accessible designed compounds and then to tune these compounds for
function. We recently disclosed success with the first of these goals.[28]Staurosporine inhibits kinase function
through hydrogen-bonding
and electrostatic interactions associated with its lactam and cationic
amine subunits.[29] Computer models suggest
that these key elements are separated by ∼9.9 Å. The roles
of the indolocarbazole and pyranyl subunits of staurosporine are less
clear but certainly conformationally restrict its binding elements.
These function-determining features are encoded in our first generation
designed analogs (Figure 6). Our first strategy
to step-economically access these analogs involved a three-component
serial cycloaddition based on an initial [5 + 2] cycloaddition that
we introduced in 1995.[30] The diene product
of that step would then be captured in a second (Diels–Alder)
cycloaddition, producing most of the target analog structure in one
operation. In fact, while the process proved less direct, this approach
did provide analogs in only seven steps with the lead analog sufficiently
potent (IC50 = 2.9 μM) to encourage further study.
Figure 6
Design
and synthesis of simplified staurosporine (PDB 1XJD) analogs[16]
Design
and synthesis of simplified staurosporine (PDB 1XJD) analogs[16]Our next iteration involved further simplification of the
analog
structure while retaining the complexity-increasing and step-decreasing
value of back-to-back cycloadditions (Figure 7). Gratifyingly, our newest analog 5 exhibits improved
potency with an IC50 value of 13 nM and improved step-economy,
being prepared in only five steps using a novel three-component, serial
[5 + 2]/[4 + 2] cycloaddition strategy.
Figure 7
Step-economical synthesis
of designed, simplified staurosporine
analog 5.
Step-economical synthesis
of designed, simplified staurosporine
analog 5.What other functions might FOS address? As exemplified above,
function
can involve binding to a target. Function can also involve target
modification. For example, complex ene-diyne natural products are
known to cleave DNA through the generation of an arene 1,4-diyl involving
a Bergman cycloaromatization.[31] Dynemicin
A is an exquisite example and reminder of the wonders of natural products.[32] Its ene-diyne subunit is encased in a 10-membered
ring incorporating a trans-epoxide that prevents
Bergman cycloaromatization. Cleavage of the epoxide, triggered by
reduction of the anthraquinone subunit, induces cycloaromatization
of the ene-diyne to an arene 1,4-diyl that abstracts hydrogens from
proximate DNA nucleotides. Based on this analysis, FOS can be used
to design simpler but effective mimics of mechanism. To mimic dynemicin
A,[33] we incorporated an epoxide-ene-diyne
subunit into a hydroisoquinoline (Figure 8)
and regulated electron density on its amine “trigger”
by attaching it to a cleavable carbonyl group. By incorporating photocleavable
or other cleavable groups on the nitrogen, one could thus control
initiation.[34] In the event, upon irradiation
in the presence of DNA, ene-diyne 6 is readily converted
to an arene 1,4-diyl, resulting in single and double strand cleavage
of DNA. An especially attractive aspect of this approach, as with
other FOS studies, is that function is achieved with step- and time-economy.
The synthesis of “photonuclease” 6 required
only eight steps.
Figure 8
A designed, simplified dynemicin A analog that cleaves
(function)
DNA.
A designed, simplified dynemicin A analog that cleaves
(function)
DNA.Are further simplifications possible?
The basis for function is
not always obvious. Upon further analysis, we came to realize that
the key to DNA cleavage (function) was not a diyl but something simpler,
an arene radical. In unrelated research, we showed that photolysis
of certain triazoles proceeds with extrusion of nitrogen and formation
of what is operationally an arene radical. When this photoextrusion
is conducted in D8-THF, one isolates a deuterated product.
In the presence of DNA, this process proceeds with DNA cleavage. To
control cleavage selectivity, we next attached a DNA recognition element
to the benzotriazole (7, Figure 9).[35] The resulting photonuclease upon
excitation caused single and double DNA strand breaks, with selective
cleavage at predominantly one site in a 167 base pair sequence.[36] While our first generation DNA cleavers required
only eight steps to make, the functional part of this this simpler
system proved to be a commercially available molecule.
Figure 9
Designed simple photonucleases
for selective DNA cleavage.
Designed simple photonucleases
for selective DNA cleavage.Beyond molecular recognition (PKC) and modification (DNA
cleavage),
another function of great significance is molecular transport, a process
pertinent to drug delivery, imaging, diagnostics, and medicine. As
illustrated previously, FOS design is often naturally inspired and
hypothesis driven. Our studies on transport started in 1997 with an
interest in drug delivery, that is, moving molecules across biological
barriers, and were inspired by the “natural product”
HIV-Tat, a protein that, unlike most, enters cells.[37]At the time, HIV-Tat’s ability to enter cells
was attributed
to its polycationic domain (Tat nine-mer: RKKRRQRRR). Our interest
was stimulated by the counterintuitive nature of this suggestion,
specifically that a polycharged, water-soluble compound would cross
a nonpolar membrane. Clearly, there were lessons to be learned. Reverse-engineering
experiments were therefore conducted to generate the information needed
to design superior, more synthetically accessible agents.[38] An arginine nine-mer was found to outperform
the Tat nine-mer. Charge type mattered: oligoarginines outperform
oligolysines. Spacing mattered: greater spaces between arginines favor
cellular uptake. Length mattered: various oligomers worked but octaarginine
is the best compromise between function (uptake) and cost of goods.
Stereochemistry mattered less: non-natural oligoarginine is better
than its enantiomer.The above reverse-engineering studies indicated
that the number
and spatial array of guanidinium groups were keys to cell entry. We
proposed that entry was initiated by hydrogen-bonding and electrostatic
association of cationic guanidinium groups with negatively charged
cell surface carboxylates, sulfates, or phosphates.[39] In one mechanistic scenario (adaptive translocation), the
cell-surface bound oligoguanidinium transporter is driven inward by
the inward polarization of the membrane potential. For larger cargos,
endocytotic pathways participate or dominate. Single molecule experiments
suggested that multiple mechanisms could operate concurrently.[37,40]The special role that we first proposed for the guanidinium
group
(hydrogen-bonding to cell-surface anions), the number of guanidinium
groups, their spatial array, and membrane potential, collectively
provided the information for the first designed cell-penetrating guanidinium-rich
transporters, peptoids with an arginine side chain attached to an
amide backbone (Figure 10).[38] We subsequently reported the first “spaced”
cell-penetrating peptides showing that spacing between side chains
influences uptake.[37] Our expectation that
more effective nonpeptidic agents could be designed led to our introduction
of the more general term “molecular transporter” (MoTr).
We have since shown that peptoids, spaced peptides, oligocarbamates,
oligocarbonates, dendrimers, and other backbones are effective (Figure 10). Impressive contributions to this rapidly growing
field from other groups have been reported in numerous reviews.[37]
Figure 10
“Natural product” inspired design of cell-penetrating
guanidinium-rich molecular transporters. P/D = probe/drug, n ≥ 5.
“Natural product” inspired design of cell-penetrating
guanidinium-rich molecular transporters. P/D = probe/drug, n ≥ 5.The beneficial impact of design on step-economy is again
apparent.
The Tat nine-mer requires ∼18 steps to make. Using a segment
doubling strategy, one achieves synthesis of octaarginine in only
9 steps and on a practical GMP scale. Finally, by employing polymer
concepts, the synthesis of guanidinium-rich oligocarbonates requires
only two steps irrespective of length. Thus, an 8-mer or a 20-mer
can be made in only two steps by controlling the initiator-to-monomer
ratio.[41]Superior function (cell entry)
is again achieved with step-economy through design.Function
extends beyond biological readouts. For example, in studies
directed at new kinase inhibitors, we developed an interest in 1,2,3-butatriene
as a reagent for one-flask back-to-back cycloadditions.[30] Enophilic cycloaddition to its 2,3-double bond
would generate a diene for a subsequent dienophilic cycloaddition.
However, butatriene is difficult to make, is unsafe to handle, and
reacts uncontrollably with most reactants. So we sought to design
a reagent that would function like butatriene but
without its liabilities. 4-(Trimethylsilyl)but-2-yn-1-ol (TMSBO, 8) fit our design criteria. Unlike butatriene, it is easily
prepared and handled. Moreover, it would be expected to engage in
ynophilic cycloadditions at its 2,3-π bond, producing, after
a vinylogous Peterson elimination, a diene for a subsequent cycloaddition.
This proved to be the case. Rhodium-catalyzed [5 + 2] cycloaddition
of commercially available vinylcyclopropane 9 and TMSBO
produced diene 10, which was captured in a second metal-catalyzed
or Diels–Alder [4 + 2] cycloaddition to produce polycycle 11 (Figure 11). This and related reagents
are now being developed in connection with cascade catalysis and multicomponent
reactions.
Figure 11
TMSBO, a reagent designed to function like butatriene
in three-component serialized cycloadditions.
TMSBO, a reagent designed to function like butatriene
in three-component serialized cycloadditions.Form follows function. Design unifies the two. Screening
of natural,
non-natural, and virtual libraries allows one to uncover structures
with known evolutionary or new functions. Known or new functions can
also be created through knowledge-driven design. Design provides choice
over form and thus whether a structure and its function would be synthetically
accessible in a step- and time-economical fashion. Chemists are uniquely
positioned to drive design utilizing knowledge of mechanism and synthesis
to create function and form in ways limited only by imagination.
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