Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB

Stopping Membrane-Enveloped Viruses with Nanotechnology Strategies: Toward Antiviral Drug Development and Pandemic Preparedness

Membrane-enveloped viruses are a leading cause of viral epidemics, and there is an outstanding need to develop broad-spectrum antiviral strategies to treat and prevent enveloped virus infections. In this review, we critically discuss why the lipid membrane surrounding enveloped virus particles is a promising antiviral target and cover the latest progress in nanotechnology research to design and evaluate membrane-targeting virus inhibition strategies. These efforts span diverse topics such as nanomaterials, self-assembly, biosensors, nanomedicine, drug delivery, and medical devices and have excellent potential to support the development of next-generation antiviral drug candidates and technologies. Application examples in the areas of human medicine and agricultural biosecurity are also presented. Looking forward, research in this direction is poised to strengthen capabilities for virus pandemic preparedness and demonstrates how nanotechnology strategies can help to solve global health challenges related to infectious diseases.

Peptides that immunoactivate the tumor microenvironment

Cancer immunotherapy has achieved positive clinical outcomes and is revolutionizing cancer treatment. However, cancer immunotherapy has thus far failed to improve outcomes for most "cold tumors", which are characterized by low infiltration of immune cells and immunosuppressive tumor microenvironment. Enhancing the responsiveness of cold tumors to cancer immunotherapy by stimulating the components of the tumor microenvironment is a strategy pursued in the last decade. Currently, most of the agents used to modify the tumor microenvironment are small molecules or antibodies. Small molecules exhibit low affinity and specificity towards the target and antibodies have shortcomings such as poor tissue penetration and high production cost. Peptides may overcome these drawbacks and therefore are promising materials for immunomodulating agents. Here we systematically summarize the currently developed immunoactivating peptides and discuss the potential of peptide therapeutics in cancer immunology.

DStabilize: A Web Resource to Generate Mirror Images of Biomolecules

Peptides comprising D-amino acids have been shown to be resistant to proteolysis. This makes them potential candidates as probes of cellular interactions, notably protein-biomolecule interactions. However, the empirical conversion of the amino acids that constitute a peptide from L-forms to D-forms will result in abrogation of the normal interactions made by the L-amino acids due to side-chain orientation changes that are associated with the changes in chirality. These interactions can be preserved by reversing the sequence of the D-peptide. We present a web server (http://dstabilize.bii.a-star.edu.sg/) that allows users to convert between L-proteins and D-proteins and for sequence reversal of D-peptides, along with the capability of performing other empirical geometric transforms. This resource allows the user to generate structures of interest easily for subsequent in silico processing.

D- and Unnatural Amino Acid Substituted Antimicrobial Peptides With Improved Proteolytic Resistance and Their Proteolytic Degradation Characteristics

The transition of antimicrobial peptides (AMPs) from the laboratory to market has been severely hindered by their instability toward proteases in biological systems. In the present study, we synthesized derivatives of the cationic AMP Pep05 (KRLFKKLLKYLRKF) by substituting L-amino acid residues with D- and unnatural amino acids, such as D-lysine, D-arginine, L-2,4-diaminobutanoic acid (Dab), L-2,3-diaminopropionic acid (Dap), L-homoarginine, 4-aminobutanoic acid (Aib), and L-thienylalanine, and evaluated their antimicrobial activities, toxicities, and stabilities toward trypsin, plasma proteases, and secreted bacterial proteases. In addition to measuring changes in the concentration of the intact peptides, LC-MS was used to identify the degradation products of the modified AMPs in the presence of trypsin and plasma proteases to determine degradation pathways and examine whether the amino acid substitutions afforded improved proteolytic resistance. The results revealed that both D- and unnatural amino acids enhanced the stabilities of the peptides toward proteases. The derivative DP06, in which all of the L-lysine and L-arginine residues were replaced by D-amino acids, displayed remarkable stability and mild toxicity in vitro but only slight activity and severe toxicity in vivo, indicating a significant difference between the in vivo and in vitro results. Unexpectedly, we found that the incorporation of a single Aib residue at the N-terminus of compound UP09 afforded remarkably enhanced plasma stability and improved activity in vivo. Hence, this derivative may represent a candidate AMP for further optimization, providing a new strategy for the design of novel AMPs with improved bioavailability.

Low Fouling Peptides with an All (d) Amino Acid Sequence Provide Enhanced Stability against Proteolytic Degradation While Maintaining Low Antifouling Properties

Peptide-functionalized surfaces, composed of optimized l-peptides, show a high resistance toward nonspecific adsorption of proteins. As l-peptides are known to be prone to proteolytic degradation, the aim of this work is to enhance the stability against enzymatic degradation by using the all d-peptide mirror image of the optimized l-peptides and to determine if the all d-enantiomer retains the protein-resistant and antifouling properties. Two l-peptides and their d-peptide mirror images, some of them containing the nonproteinogenic amino acid α-aminoisobutyric acid (Aib), were synthesized and tested against non-specific adsorption of the proteins lysozyme and fibrinogen and the settlement of marine diatom Navicula perminuta and marine bacteria Cobetia marina. Both the d-enantiomer and the insertion of Aib protected the peptides from proteolytic degradation. Protein resistance was enhanced with the d-enantiomers while maintaining the resistance toward diatoms.

Chiral Protein Supraparticles for Tumor Suppression and Synergistic Immunotherapy: An Enabling Strategy for Bioactive Supramolecular Chirality Construction

The design of bioactive supramolecular chirality is always hampered by the lack of feasible schemes to assigned specific biological activities. Herein, we developed a "mirror-image peptide grafting" method to graft the epitopes of bioactive d-peptide onto the miniprotein template to construct a self-assembled supraparticle. Grafting ^DPMI^β, a 12-mer d-enantiomeric peptide functioned as the p53 agonist, onto Apamin, we successfully constructed a self-assembled d-enantiomeric miniprotein supermolecule nanoparticle, termed ^DMSN. This chiral supraparticle possesses a favorable pharmaceutical profile including the passive tumor targeting, cell membrane penetration, intracellular reductive responsiveness, and endosome escaping. ^DMSN showed in vitro and in vivo p53-dependent antiproliferative activity and augmented antitumor immunity elicited by anti-PD1 therapy. This enabling strategy will allow us to fabricate a class of peptide/protein-derived supramolecular chirality with predictable biological activities and will likely have a broad impact on the chiral nanotechnology at the service of prevention and treatment of human diseases.

Macrocyclization of an all-d linear α-helical peptide imparts cellular permeability

Peptide-based molecules hold great potential as targeted inhibitors of intracellular protein-protein interactions (PPIs). Indeed, the vast diversity of chemical space conferred through their primary, secondary and tertiary structures allows these molecules to be applied to targets that are typically deemed intractable via small molecules. However, the development of peptide therapeutics has been hindered by their limited conformational stability, proteolytic sensitivity and cell permeability. Several contemporary peptide design strategies are aimed at addressing these issues. Strategic macrocyclization through optimally placed chemical braces such as olefinic hydrocarbon crosslinks, commonly referred to as staples, may improve peptide properties by (i) restricting conformational freedom to improve target affinities, (ii) improving proteolytic resistance, and (iii) enhancing cell permeability. As a second strategy, molecules constructed entirely from d-amino acids are hyper-resistant to proteolytic cleavage, but generally lack conformational stability and membrane permeability. Since neither approach is a complete solution, we have combined these strategies to identify the first examples of all-d α-helical stapled and stitched peptides. As a template, we used a recently reported all d-linear peptide that is a potent inhibitor of the p53-Mdm2 interaction, but is devoid of cellular activity. To design both stapled and stitched all-d-peptide analogues, we used computational modelling to predict optimal staple placement. The resultant novel macrocyclic all d-peptide was determined to exhibit increased α-helicity, improved target binding, complete proteolytic stability and, most notably, cellular activity.

Methods to Enhance the Metabolic Stability of Peptide-Based PET Radiopharmaceuticals

The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of many peptide-based pharmaceuticals, including peptide-based positron emission tomography (PET) radiopharmaceuticals. However, the poor in vivo stability of unmodified peptides against proteolysis is a major challenge that must be overcome, as it can result in an impractically short in vivo biological half-life and a subsequently poor bioavailability when used in imaging and therapeutic applications. Consequently, many biologically and pharmacologically interesting peptide-based drugs may never see application. A potential way to overcome this is using peptide analogues designed to mimic the pharmacophore of a native peptide while also containing unnatural modifications that act to maintain or improve the pharmacological properties. This review explores strategies that have been developed to increase the metabolic stability of peptide-based pharmaceuticals. It includes modifications of the C- and/or N-termini, introduction of d- or other unnatural amino acids, backbone modification, PEGylation and alkyl chain incorporation, cyclization and peptide bond substitution, and where those strategies have been, or could be, applied to PET peptide-based radiopharmaceuticals.

DPepH3, an Improved Peptide Shuttle for Receptor-independent Transport Across the Blood-Brain Barrier

Background:

The use of peptides as drug carriers across the blood-brain barrier (BBB) has increased significantly during the last decades. PepH3, a seven residue sequence (AGILKRW) derived from the α-helical domain of the dengue virus type-2 capsid protein, translocates across the BBB with very low toxicity. Somehow predictably from its size and sequence, PepH3 is degraded in serum relatively fast. Among strategies to increase peptide half-life (t1/2), the use of the enantiomer (wholly made of D-amino acid residues) can be quite successful if the peptide interacts with a target in non-stereospecific fashion.

Methods:

The goal of this work was the development of a more proteolytic-resistant peptide, while keeping the translocation properties. The serum stability, cytotoxicity, in vitro BBB translocation, and internalization mechanism of DPepH3 was assessed and compared to the native peptide.

Results:

DPepH3 demonstrates a much longer t1/2 compared to PepH3. We also confirm that BBB translocation is receptor-independent, which fully validates the enantiomer strategy chosen. In fact, we demonstrate that internalization occurs trough macropinocytosis. In addition, the enantiomer demonstrates to be non-cytotoxic towards endothelial cells as PepH3.

Conclusion:

DPepH3 shows excellent translocation and internalization properties, safety, and improved stability. Taken together, our results place DPepH3 at the forefront of the second generation of BBB shuttles.

Soft Nanoarchitectonics for Enantioselective Biosensing

Chirality is a fundamental property of a molecule, and the significant progress in chirality detection and quantification of a molecule has inspired major advances in various fields ranging from chemistry, biology, to biotechnology and pharmacology. Chiral molecules have identical molecular formulas, atom-to-atom linkages, and bonding distances, and as such they are difficult to distinguish both sensitively and selectively. Today, most new drugs and those under development are chiral, which requires technological developments in the separation and detection of chiral molecules. Therefore, rapid and facile methods to detect and discriminate chiral compounds are necessary to accelerate advances in many research fields. The challenges in analysis stem from the obvious fact that chiral molecules have the same physical properties. Although significant progress on the detection of enantiomeric composition has been achieved in the past decade, in order to fully realize the capacity of chiral molecular interrogation, highly sensitive and selective, portable, and easy-to-use detection remains challenging because of the limitation of conventional techniques.Soft nanoarchitectonics is a new concept for the fabrication of functional soft material systems through harmonization of various actions including atomic/molecular-level manipulation, chemical reactions, self-assembly and self-organization, and their modulation by external fields/stimuli. Soft nanoarchitectonics has been widely used as a key enabling technology for integrating predefined molecular functionalities including electrochemical, optical, catalytic, or biological properties into biosensing devices, which provides exciting opportunities to design, assemble, and fabricate tailored nanosystems to enable new sensing strategies for chiral molecules.In this Account, we aim to concisely discuss how these molecule-inspired soft nanoarchitectonics work for enantioselective sensing. We will first outline the basic principle and mechanistic insights of the soft nanoarchitectonics approach for enantioselective sensing, and then we will describe the new breakthroughs and trends in the area that have been most recently reported by our groups and others. There will also be a discussion on the merits of soft nanoarchitectonics based sensing in comparison to conventional analytical methods. Finally, with this Account, we hope to spark new chiral molecule sensing strategies by fundamentally understanding chiral recognition and engineering soft nanoarchitectonics with programmable structures and predictable sensing properties.

Complete identification of all 20 relevant epimeric peptides in β-amyloid: a new HPLC-MS based analytical strategy for Alzheimer's research

Although the underlying cause of Alzheimer's disease (AD) is not known, the extracellular deposition of β-amyloid (Aβ) is considered as a hallmark of AD brains. Evidence has shown the occurrence of d-Asp, isoAsp, and d-Ser residues in Aβ, which may be indicative of and/or contribute to the neurodegeneration in AD patients. Herein, we have developed the first high-throughput profiling technique for all 20 isobaric Aβ peptide epimers containing Asp, isoAsp, and Ser isomers using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). This new analytical strategy allows the direct detection and identification of all possible Asp, isoAsp, and Ser stereoisomers in Aβ, and may contribute to a better understanding of the pathogenesis of AD.

Peptide science: A "rule model" for new generations of peptidomimetics

Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.

Is the Mirror Image a True Reflection? Intrinsic Membrane Chirality Modulates Peptide Binding

Peptides with pharmaceutical activities are attractive drug leads, and knowledge of their mode-of-action is essential for translation into the clinic. Comparison of native and enantiomeric peptides has long been used as a powerful approach to discriminate membrane- or receptor-mediated modes-of-action on the basis of the assumption that interactions with cell membranes are independent of peptide chirality. Here, we revisit this paradigm with the cyclotide kalata B1, a drug scaffold with intrinsic membrane-binding activity whose enantiomer is less potent than native peptide. To investigate this chirality dependence, we compared peptide-lipid binding using mirror image model membranes. We synthesized phospholipids with non-natural chirality and demonstrate that native kalata B1 binds with higher affinity to phospholipids with chirality found in eukaryotic membranes. This study shows for the first time that the chiral environment of lipid bilayers can modulate the function of membrane-active peptides and challenges the view that peptide-lipid interactions are achiral.

Molecular basis for chirality-regulated Aβ self-assembly and receptor recognition revealed by ion mobility-mass spectrometry

Despite extensive efforts on probing the mechanism of Alzheimer’s disease (AD) and enormous investments into AD drug development, the lack of effective disease-modifying therapeutics and the complexity of the AD pathogenesis process suggest a great need for further insights into alternative AD drug targets. Herein, we focus on the chiral effects of truncated amyloid beta (Aβ) and offer further structural and molecular evidence for epitope region-specific, chirality-regulated Aβ fragment self-assembly and its potential impact on receptor-recognition. A multidimensional ion mobility-mass spectrometry (IM-MS) analytical platform and in-solution kinetics analysis reveal the comprehensive structural and molecular basis for differential Aβ fragment chiral chemistry, including the differential and cooperative roles of chiral Aβ N-terminal and C-terminal fragments in receptor recognition. Our method is applicable to many other systems and the results may shed light on the potential development of novel AD therapeutic strategies based on targeting the D-isomerized Aβ, rather than natural L-Aβ.

Chiral inversion of amino acids is thought to modulate the structure and function of amyloid beta (Aβ) but these processes are poorly understood. Here, the authors develop an ion mobility-mass spectrometry based approach to study chirality-regulated structural features of Aβ fragments and their influence on receptor recognition.

Computational investigation of retro-isomer equilibrium structures: Intrinsically disordered, foldable, and cyclic peptides

We use all-atom modeling and advanced-sampling molecular dynamics simulations to investigate quantitatively the effect of peptide bond directionality on the equilibrium structures of four linear (two foldable, two disordered) and two cyclic peptides. We find that the retro forms of cyclic and foldable linear peptides adopt distinctively different conformations compared to their parents. While the retro form of a linear intrinsically disordered peptide with transient secondary structure fails to reproduce a secondary structure content similar to that of its parent, the retro form of a shorter disordered linear peptide shows only minor differences compared to its parent.

The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies

Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.

Mirror image pairs of cyclic hexapeptides have different oral bioavailabilities and metabolic stabilities

Rule-of-five parameters and membrane permeabilities are not the only determinants of oral bioavailability.

Targeting vesicle size

An amphipathic peptide has been engineered and is capable of penetrating the blood–brain barrier as well as possessing a potent antiviral activity against Zika and other mosquito-borne viruses.

Therapeutic treatment of Zika virus infection using a brain-penetrating antiviral peptide

Zika virus is a mosquito-borne virus that is associated with neurodegenerative diseases, including Guillain-Barré syndrome¹ and congenital Zika syndrome². As Zika virus targets the nervous system, there is an urgent need to develop therapeutic strategies that inhibit Zika virus infection in the brain. Here, we have engineered a brain-penetrating peptide that works against Zika virus and other mosquito-borne viruses. We evaluated the therapeutic efficacy of the peptide in a lethal Zika virus mouse model exhibiting systemic and brain infection. Therapeutic treatment protected against mortality and markedly reduced clinical symptoms, viral loads and neuroinflammation, as well as mitigated microgliosis, neurodegeneration and brain damage. In addition to controlling systemic infection, the peptide crossed the blood-brain barrier to reduce viral loads in the brain and protected against Zika-virus-induced blood-brain barrier injury. Our findings demonstrate how engineering strategies can be applied to develop peptide therapeutics and support the potential of a brain-penetrating peptide to treat neurotropic viral infections.

Solid-Phase Total Synthesis and Dual Mechanism of Action of the Channel-Forming 48-mer Peptide Polytheonamide B

Polytheonamide B (1) is a unique peptide natural product because of its extremely complex structure, a channel-forming ability in vitro, and the extremely potent cytotoxicity. The 48-mer sequence of 1 comprises alternating d,l-amino acids and possesses an array of sterically bulky β-tetrasubstituted and hydrogen bond forming residues. These unusual structural features are believed to drive 1 to fold into a 4.5 nm long tube, form a transmembrane ion channel at the plasma membrane, and exert cytotoxicity. Despite its potential biological application, however, multiple substitutions by these unusual residues significantly heightened the synthetic challenges, impeding the solid-phase peptide synthesis (SPPS) of 1. In this study, we first addressed the synthesis problem by extensive optimization of various factors of the SPPS. Adaptation of a new protective group strategy allowed for elongation of a 37-mer peptide on resin, to which an N-terminal 11-mer fragment was condensed. Removal of the 18 protective groups and resin gave rise to 1 in excellent overall yield (4.5%, 76 steps from 17). The SPPS protocol is operationally simple and was proven easily amenable to total synthesis of the fluorescent 48-mer probe 2. Synthetic 1 and 2 were utilized for analysis of their cellular behavior. Reflecting its ion-channel function, the addition of 1 to MCF-7 cells rapidly diminished a potential across the plasma membrane. Furthermore, fluorescence imaging study revealed that 1 and 2 were also internalized into the cells, accumulating in acidic lysosomes and neutralizing the lysosomal pH gradient. These new findings indicated that 1 is capable of exerting two functions upon causing apoptotic cell death of mammalian cells: It induces free cation transport across the plasma as well as lysosomal membranes. The present chemical and biological studies provide valuable information for the design and synthesis of polytheonamide-based molecules with more potent and selective biological activities.

Xenoprotein engineering via synthetic libraries

Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.

The present and the future of motif-mediated protein-protein interactions

Protein-protein interactions (PPIs) are essential to governing virtually all cellular processes. Of particular importance are the versatile motif-mediated interactions (MMIs), which are thus far underrepresented in available interaction data. This is largely due to technical difficulties inherent in the properties of MMIs, but due to the increasing recognition of the vital roles of MMIs in biology, several systematic approaches have recently been developed to detect novel MMIs. Consequently, rapidly growing numbers of motifs are being identified and pursued further for therapeutic applications. In this review, we discuss the current understanding on the diverse functions and disease-relevance of MMIs, the key methodologies for detection of MMIs, and the potential of MMIs for drug development.

What are the drugs of the future?

Are small molecules or biologics the drugs of the future? Small-molecule drugs have historically been the pillars of traditional medicine. However, recently, we seem to be amidst a scientific revolution with the rise of many FDA-approved biologic drugs. This opinion article looks at the current state of small molecules and biologics and assesses what the future holds for these two broad classes of drugs.

Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein⁻Protein Interactions

Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.

Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions

Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive natural product structural framework (reasonable chaos), can be directed to confer dynamically new protein–ligand interactions beyond the basic lock–key model (imaginative order). Here we summarise our work on exploring conformational diversity from fluorinated natural product fragments, and how this approach of conformation-coupled diversity-oriented synthesis can be used to iteratively derive ligands with enhanced specificity against highly homologous protein domains. Our results demonstrate that the conformation entropic states of highly conserved protein domains differ significantly, and this conformational diversity, beyond primary sequence analysis, can be duly captured and exploited by natural-product derived ligands with complementary conformational dynamics for enhancing recognition specificity in drug lead discovery.