Protein conformational studies for macromolecularly imprinted polymers

Molecular imprinting technology for biomedical applications

Molecularly imprinted polymers (MIPs), a type of biomimetic material, have attracted considerable interest owing to their cost-effectiveness, good physiochemical stability, favourable specificity and selectivity for target analytes, and widely used for various biological applications. It was demonstrated that MIPs with significant selectivity towards protein-based targets could be applied in medicine, diagnostics, proteomics, environmental analysis, sensors, various in vivo and/or in vitro applications, drug delivery systems, etc. This review provides an overview of MIPs dedicated to biomedical applications and insights into perspectives on the application of MIPs in newly emerging areas of biotechnology. Many different protocols applied for the synthesis of MIPs are overviewed in this review. The templates used for molecular imprinting vary from the minor glycosylated glycan-based structures, amino acids, and proteins to whole bacteria, which are also overviewed in this review. Economic, environmental, rapid preparation, stability, and reproducibility have been highlighted as significant advantages of MIPs. Particularly, some specialized MIPs, in addition to molecular recognition properties, can have high catalytic activity, which in some cases could be compared with other bio-catalytic systems. Therefore, such MIPs belong to the class of so-called 'artificial enzymes'. The discussion provided in this manuscript furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages highlighting trends and possible future directions of MIP technology.

Bovine Serum Albumin Molecularly Imprinted Electrochemical Sensors Modified by Carboxylated Multi-Walled Carbon Nanotubes/CaAlg Hydrogels

In this paper, sodium alginate (NaAlg) was used as functional monomers, bovine serum albumin (BSA) was used as template molecules, and calcium chloride (CaCl2) aqueous solution was used as a cross-linking agent to prepare BSA molecularly imprinted carboxylated multi-wall carbon nanotubes (CMWCNT)/CaAlg hydrogel films (MIPs) and non-imprinted hydrogel films (NIPs). The adsorption capacity of the MIP film for BSA was 27.23 mg/g and the imprinting efficiency was 2.73. The MIP and NIP hydrogel film were loaded on the surface of the printed electrode, and electrochemical performance tests were carried out by electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV) using the electrochemical workstation. The loaded MIP film and NIP film effectively improved the electrochemical signal of the bare carbon electrode. When the pH value of the Tris HCl elution solution was 7.4, the elution time was 15 min and the adsorption time was 15 min, and the peak currents of MIP-modified electrodes and NIP-modified electrodes reached their maximum values. There was a specific interaction between MIP-modified electrodes and BSA, exhibiting specific recognition for BSA. In addition, the MIP-modified electrodes had good anti-interference, reusability, stability, and reproducibility. The detection limit (LOD) was 5.6 × 10-6 mg mL-1.

Molecularly Imprinted Polymer-Based Sensors for Protein Detection

The accurate detection of biological substances such as proteins has always been a hot topic in scientific research. Biomimetic sensors seek to imitate sensitive and selective mechanisms of biological systems and integrate these traits into applicable sensing platforms. Molecular imprinting technology has been extensively practiced in many domains, where it can produce various molecular recognition materials with specific recognition capabilities. Molecularly imprinted polymers (MIPs), dubbed plastic antibodies, are artificial receptors with high-affinity binding sites for a particular molecule or compound. MIPs for protein recognition are expected to have high affinity via numerous interactions between polymer matrices and multiple functional groups of the target protein. This critical review briefly describes recent advances in the synthesis, characterization, and application of MIP-based sensor platforms used to detect proteins.

Development of molecularly imprinted polymer based phase boundaries for sensors design (review)

Achievements in polymer chemistry enables to design artificial phase boundaries modified by imprints of selected molecules and some larger structures. These structures seem very useful for the design of new materials suitable for affinity chromatography and sensors. In this review, we are overviewing the synthesis of molecularly imprinted polymers (MIPs) and the applicability of these MIPs in the design of affinity sensors. Such MIP-based layers or particles can be used as analyte-recognizing parts for sensors and in some cases they can replace very expensive compounds (e.g.: antibodies, receptors etc.), which are recognizing analyte. Many different polymers can be used for the formation of MIPs, but conducing polymers shows the most attractive capabilities for molecular-imprinting by various chemical compounds. Therefore, the application of conducting polymers (e.g.: polypyrrole, polyaniline, polythiophene, poly(3,4-ethylenedioxythiophene), and ortho-phenylenediamine) seems very promising. Polypyrrole is one of the most suitable for the development of MIP-based structures with molecular imprints by analytes of various molecular weights. Overoxiation of polypyrrole enables to increase the selectivity of polypyrrole-based MIPs. Methods used for the synthesis of conducting polymer based MIPs are overviewed. Some methods, which are applied for the transduction of analytical signal, are discussed, and challenges and new trends in MIP-technology are foreseen.

Electrochemically Deposited Molecularly Imprinted Polymer-Based Sensors

This review is dedicated to the development of molecularly imprinted polymers (MIPs) and the application of MIPs in sensor design. MIP-based biological recognition parts can replace receptors or antibodies, which are rather expensive. Conducting polymers show unique properties that are applicable in sensor design. Therefore, MIP-based conducting polymers, including polypyrrole, polythiophene, poly(3,4-ethylenedioxythiophene), polyaniline and ortho-phenylenediamine are frequently applied in sensor design. Some other materials that can be molecularly imprinted are also overviewed in this review. Among many imprintable materials conducting polymer, polypyrrole is one of the most suitable for molecular imprinting of various targets ranging from small organics up to rather large proteins. Some attention in this review is dedicated to overview methods applied to design MIP-based sensing structures. Some attention is dedicated to the physicochemical methods applied for the transduction of analytical signals. Expected new trends and horizons in the application of MIP-based structures are also discussed.

Peptide epitope-imprinted polymer microarrays for selective protein recognition. Application for SARS-CoV-2 RBD protein

We introduce a practically generic approach for the generation of epitope-imprinted polymer-based microarrays for protein recognition on surface plasmon resonance imaging (SPRi) chips. The SPRi platform allows the subsequent rapid screening of target binding kinetics in a multiplexed and label-free manner. The versatility of such microarrays, both as synthetic and screening platform, is demonstrated through developing highly affine molecularly imprinted polymers (MIPs) for the recognition of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. A characteristic nonapeptide GFNCYFPLQ from the RBD and other control peptides were microspotted onto gold SPRi chips followed by the electrosynthesis of a polyscopoletin nanofilm to generate in one step MIP arrays. A single chip screening of essential synthesis parameters, including the surface density of the template peptide and its sequence led to MIPs with dissociation constants (K D) in the lower nanomolar range for RBD, which exceeds the affinity of RBD for its natural target, angiotensin-convertase 2 enzyme. Remarkably, the same MIPs bound SARS-CoV-2 virus like particles with even higher affinity along with excellent discrimination of influenza A (H3N2) virus. While MIPs prepared with a truncated heptapeptide template GFNCYFP showed only a slightly decreased affinity for RBD, a single mismatch in the amino acid sequence of the template, i.e. the substitution of the central cysteine with a serine, fully suppressed the RBD binding.

Artificial Biomimetic Electrochemical Assemblies

Rapid, selective, and cost-effective detection and determination of clinically relevant biomolecule analytes for a better understanding of biological and physiological functions are becoming increasingly prominent. In this regard, biosensors represent a powerful tool to meet these requirements. Recent decades have seen biosensors gaining popularity due to their ability to design sensor platforms that are selective to determine target analytes. Naturally generated receptor units have a high affinity for their targets, which provides the selectivity of a device. However, such receptors are subject to instability under harsh environmental conditions and have consequently low durability. By applying principles of supramolecular chemistry, molecularly imprinted polymers (MIPs) can successfully replace natural receptors to circumvent these shortcomings. This review summarizes the recent achievements and analytical applications of electrosynthesized MIPs, in particular, for the detection of protein-based biomarkers. The scope of this review also includes the background behind electrochemical readouts and the origin of the gate effect in MIP-based biosensors.

Constructing High-Recognition Protein-Imprinted Materials Using "Specially Designed" Block Macromolecular Chains as Functional Monomers and Crosslinkers

The use of a macromolecularly functional monomer and crosslinker (MFM) to stabilize and imprint a template protein is a new method to construct high-recognition protein-imprinted materials. In this study, for the first time, a "specially designed" block MFM with both "functional capability" and "crosslinking capability" segments was synthesized via reversible addition-fragmentation chain-transfer polymerization and used to fabricate bovine serum albumin (BSA)-imprinted microspheres (SiO₂@MPS@MIPs-MFM) by the surface imprinting strategy. Results from circular dichroic spectrum experiments reflected that the block MFM could maintain the natural form of BSA, whereas its corresponding and equivalent micromolecularly functional monomer (MIM) seriously destroyed the secondary structure of proteins. Batch rebinding experiments showed that the maximum adsorption capacity and imprinting factor of SiO₂@MPS@MIPs-MFM reached 314.9 mg g^-1 and 4.02, which were significantly superior to that of MIM-based imprinted materials. In addition, since the crosslinking capability segments in block MFM involved zwitterionic functional groups with a protein-repelling effect, SiO₂@MPS@MIPs-MFM showed better specific rebinding ability than the imprinted material prepared by MFM without this component. Besides, scanning electron microscopy and transmission electron microscopy images showed that the shell thickness of SiO₂@MPS@MIPs-MFM was approximately 15 nm, and such a thin imprinted layer ensured its rapid adsorption equilibrium (120 min). As a result, SiO₂@MPS@MIPs-MFM revealed fantastic selectivity and recognition ability in a mixed protein solution and could efficiently extract BSA from biological samples of bovine calf serum. The proposal of block MFM enriched the options and designability of monomers in protein imprinting technology, thereby laying a foundation for developing high-performance protein-imprinted materials.

Advances in Molecularly Imprinted Polymers Based Affinity Sensors (Review)

Recent challenges in biomedical diagnostics show that the development of rapid affinity sensors is very important issue. Therefore, in this review we are aiming to outline the most important directions of affinity sensors where polymer-based semiconducting materials are applied. Progress in formation and development of such materials is overviewed and discussed. Some applicability aspects of conducting polymers in the design of affinity sensors are presented. The main attention is focused on bioanalytical application of conducting polymers such as polypyrrole, polyaniline, polythiophene and poly(3,4-ethylenedioxythiophene) ortho-phenylenediamine. In addition, some other polymers and inorganic materials that are suitable for molecular imprinting technology are also overviewed. Polymerization techniques, which are the most suitable for the development of composite structures suitable for affinity sensors are presented. Analytical signal transduction methods applied in affinity sensors based on polymer-based semiconducting materials are discussed. In this review the most attention is focused on the development and application of molecularly imprinted polymer-based structures, which can replace antibodies, receptors, and many others expensive affinity reagents. The applicability of electrochromic polymers in affinity sensor design is envisaged. Sufficient biocompatibility of some conducting polymers enables to apply them as "stealth coatings" in the future implantable affinity-sensors. Some new perspectives and trends in analytical application of polymer-based semiconducting materials are highlighted.

Does the protein corona take over the selectivity of molecularly imprinted nanoparticles? The biological challenges to recognition

"Plastic antibodies" are nano-sized biomimetics prepared by the molecular imprinting technology, which have the robustness of polymers, but specificity and selectivity alike natural receptors making them ideal for analytical uses. The current challenge is to translate plastic antibodies to in vivo applications for diagnosis, drug delivery, theranostic, therefore it is crucial to evaluate the effect of the biological sample complexity on the selectivity and the formation of protein corona (PCs), which ultimately dictate the fate of circulating nanoparticles. A set (n = 4) of plastic antibodies (nanoMIPs) against different proteins was prepared. Quantitative (iBAC) shotgun proteomics permitted to define the PC composition of nanoMIPs in human plasma, the relative protein abundances, the correlation between PC and the plasma dilution. NanoMIPs showed >200 proteins PC, while ~150 proteins were found on controls, suggesting the imprinting process influences the nanoparticle's structure hence the protein uptake. NanoMIPs and controls shared the 44% of the PC, but PC iBAQ values on nanoMIPs were 10-100 times higher than controls, suggesting PC/nanoMIPs interactions were far stronger than PC/non imprinted particles. PCs were richer in small proteins and in immunoglobulins, indicating a defensive response, while the selectivity was negatively challenged in the crowded plasma sample. SIGNIFICANCE: The formation and the composition of the protein corona (PC) is key to decide the fate of nanoparticles when in vivo, therefore there is the strong need to study the composition of the PC. To enable and to support the translation of the use of plastic antibodies (nanoMIPs), prepared by means of the molecular imprinting technique, to the clinical practice and to in vivo uses, the present work evaluates the effects of the complexity of the biological sample (plasma) on nanoMIPs composed of highly crosslinked polyacrylamide and acrylamide derivatives. Proteomic study offers an in depth insight of the protein corona formed in plasma on nanoMIPs. A set of nanoMIPs synthesized and raised to recognize either small or large proteins was tested. The selection abilities of the nanoMIPs when placed in plasma at different dilutions was studied. Quantitative shotgun proteomics allowed to define the composition of the formed protein corona (PC) enabling to detail the protein compositions, the relative abundances, its correlation to the biological sample composition and the correlation between PC and nanoMIP's imprinted template. In plasma, all the nanoMIPs gained a PC composed of more than 200 proteins. Type of protein recruited for the corona, molecular weight and abundance in the PC were studied. The PC on the nanoMIPs appeared to be driven by the protein composition of the plasma, while the template protein, towards which a nanoMIP was imprinted and that was proven to have high affinity for, did not influence the PC.

Molecular recognition with soft biomaterials

Biomacromolecules and engineered materials can achieve molecular recognition if they engage their ligand with properly oriented and chemically complementary moieties. Recently, there has been significant interest in fabricating recognitive soft materials, which possess specific affinity for biological analytes. We present a summary and evaluation of current recognitive materials for biosensing, drug delivery, and regenerative medicine applications. We highlight the impact of material composition on the extent and specificity of ligand adsorption, citing new theoretical and empirical evidence. We conclude with a guide for synthesizing and characterizing novel recognitive materials, as well as recommendations for ligand selection and experimental design.

Electrochemical MIP Sensor for Butyrylcholinesterase

Molecularly imprinted polymers (MIPs) mimic the binding sites of antibodies by substituting the amino acid-scaffold of proteins by synthetic polymers. In this work, the first MIP for the recognition of the diagnostically relevant enzyme butyrylcholinesterase (BuChE) is presented. The MIP was prepared using electropolymerization of the functional monomer o-phenylenediamine and was deposited as a thin film on a glassy carbon electrode by oxidative potentiodynamic polymerization. Rebinding and removal of the template were detected by cyclic voltammetry using ferricyanide as a redox marker. Furthermore, the enzymatic activity of BuChE rebound to the MIP was measured via the anodic oxidation of thiocholine, the reaction product of butyrylthiocholine. The response was linear between 50 pM and 2 nM concentrations of BuChE with a detection limit of 14.7 pM. In addition to the high sensitivity for BuChE, the sensor responded towards pseudo-irreversible inhibitors in the lower mM range.

New protocol for optimisation of polymer composition for imprinting of peptides and proteins

A novel screening tool for high-throughput optimisation of monomer composition for imprinting of peptides and proteins.

Recognition of protein biomarkers using epitope-mediated molecularly imprinted films: Histidine or cysteine modified epitopes?

This research aims to engineer molecularly imprinted polymer (MIP)-based synthetic receptors for the molecular recognition of neuron specific enolase (NSE) biomarker. The synthetic peptide derived from the NSE was synthesized along with its cysteine and histidine modified versions. The modified peptides were utilized as templates for molecular imprinting, which was achieved by combination of epitope- and electrochemical surface imprinting strategy. The subsequently generated imprinted cavities were used for the detection of the NSE derived peptide and NSE. The imprints created with cysteine (CME) and histidine modified epitopes (HME) could detect the peptide in a concentration range of 2-128 µM and 15.6 nM to 128 µM, respectively. The recognition of NSE was achieved by the same imprints in a linear range of 1-64 ng mL^-1 (CME) and 0.25-64 ng mL^-1 (HME), respectively. The target molecules bound to the control polymer very weakly, confirming the high selectivity of the MIP cavities. Selectivity studies resulted in imprinting factors of 8.8 and 11 for the CME and HME imprints, respectively. The affinity analyses provided dissociation constants of 2.3 × 10^-10 M and 3 × 10^-11 M for NSE recognition using the corresponding epitope imprints. Cross-reactivity studies with non-specific molecules proved high specificity of the artificial receptors for the targets.

Turn-on fluorescence detection of protein by molecularly imprinted hydrogels based on supramolecular assembly of peptide multi-functional blocks

Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (α = 1.25) and lysozyme (α = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Δτ = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.

Protein-Imprinted Polymers: The Shape of Things to Come?

The potential to develop materials with antibody-like molecular recognition properties has helped sustain interest in protein-imprinted polymers over the past several decades. Unfortunately, despite persistent research, the field of noncovalent protein imprinting has seen limited success in terms of achieving materials with high selectivity and high affinity. In this Perspective, important yet sometimes overlooked aspects of the imprinting and binding processes are reviewed to help understand why there has been limited success. In particular, the imprinting and binding processes are viewed through the scope of free radical polymerization and hydrogel swelling theories to underscore the complexity of the synthesis and behavior of protein-imprinted polymers. Additionally, we review the metrics of success commonly used in protein imprinting literature (i.e., adsorption capacity, imprinting factor, and selectivity factor) and consider the relevance of each to the characterization of an imprinted polymer's recognition characteristics. Throughout, common shortcomings are highlighted, and experiments that could help verify or disprove the efficacy of noncovalent protein imprinting are discussed.

Student award for outstanding research winner in the Ph.D. category for the 2017 society for biomaterials annual meeting and exposition, april 5-8, 2017, Minneapolis, Minnesota: Characterization of protein interactions with molecularly imprinted hydrogels that possess engineered affinity for high isoelectric point biomarkers

Molecularly imprinted polymers (MIPs) with selective affinity for protein biomarkers could find extensive utility as environmentally robust, cost-efficient biomaterials for diagnostic and therapeutic applications. In order to develop recognitive, synthetic biomaterials for prohibitively expensive protein biomarkers, we have developed a molecular imprinting technique that utilizes structurally similar, analogue proteins. Hydrogel microparticles synthesized by molecular imprinting with trypsin, lysozyme, and cytochrome c possessed an increased affinity for alternate high isoelectric point biomarkers both in isolation and plasma-mimicking adsorption conditions. Imprinted and non-imprinted P(MAA-co-AAm-co-DEAEMA) microgels containing PMAO-PEGMA functionalized polycaprolactone nanoparticles were net-anionic, polydisperse, and irregularly shaped. MIPs and control non-imprinted polymers (NIPs) exhibited regions of Freundlich and BET isotherm adsorption behavior in a range of non-competitive protein solutions, where MIPs exhibited enhanced adsorption capacity in the Freundlich isotherm regions. In a competitive condition, imprinting with analogue templates (trypsin, lysozyme) increased the adsorption capacity of microgels for cytochrome c by 162% and 219%, respectively, as compared to a 122% increase provided by traditional bulk imprinting with cytochrome c. Our results suggest that molecular imprinting with analogue protein templates is a viable synthetic strategy for enhancing hydrogel-biomarker affinity and promoting specific protein adsorption behavior in biological fluids. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1565-1574, 2017.

Selective extraction of proteins and other macromolecules from biological samples using molecular imprinted polymers

The accurate determination of intact macromolecules in biological samples, such as blood, plasma, serum, urine, tissue and feces is a challenging problem. The increased interest in macromolecules both as candidate drugs and as biomarkers for diagnostic purposes means that new method development approaches are needed. This review charts developments in the use of molecularly imprinted polymers first for small-molecular-mass compounds then for proteins and other macromolecules. Examples of the development of molecularly imprinted polymers for macromolecules are highlighted. The two main application areas to date are sensors and separation science, particularly SPE. Examples include peptides and polypeptides, lysozyme, hemoglobin, ovalbumin, bovine serum albumin and viruses.

Guided folding takes a start from the molecular imprinting of structured epitopes

A biomimetic route towards assisted folding was explored. Molecularly imprinted polymeric nanoparticles (MIP NPs), i.e. biomimetics with entailed molecular recognition properties made by a template assisted synthesis, were prepared to target a structured epitope: the cystine containing peptide CC9ox, which corresponds to the apical portion of the β-hairpin hormone Hepcidin-25. The structural selection was achieved by the MIP NPs; moreover, the MIP NPs demonstrated favouring the folding of the linear random peptide (CC9red) into the structured one (CC9ox), anticipating the future role of the MIP NPs as in situ nanomachines to counteract folding defects.

Transforming the blood glucose meter into a general healthcare meter for in vitro diagnostics in mobile health

Recent advances in mobile network and smartphones have provided an enormous opportunity for transforming in vitro diagnostics (IVD) from central labs to home or other points of care (POC). A major challenge to achieving the goal is a long time and high costs associated with developing POC IVD devices in mobile Health (mHealth). Instead of developing a new POC device for every new IVD target, we and others are taking advantage of decades of research, development, engineering and continuous improvement of the blood glucose meter (BGM), including those already integrated with smartphones, and transforming the BGM into a general healthcare meter for POC IVDs of a wide range of biomarkers, therapeutic drugs and other analytical targets. In this review, we summarize methods to transduce and amplify selective binding of targets by antibodies, DNA/RNA aptamers, DNAzyme/ribozymes and protein enzymes into signals such as glucose or NADH that can be measured by commercially available BGM, making it possible to adapt many clinical assays performed in central labs, such as immunoassays, aptamer/DNAzyme assays, molecular diagnostic assays, and enzymatic activity assays onto BGM platform for quantification of non-glucose targets for a wide variety of IVDs in mHealth.

The challenge to improve the response of biomaterials to the physiological environment

New applications of biomaterials often require advanced structures containing synthetic and natural components that are tuned to provide properties unique to a specific application. We discuss how structural characteristics of biomaterials, especially hydrophilic ones, can be used in conjunction with non-ideal thermodynamics to develop advanced medical systems. We show a number of examples of biocompatible, intelligent biomaterials that can be used for organ replacement, biosensors, precise drug delivery over days or weeks, and regenerative medicine.

Analytical applications of MIPs in diagnostic assays: future perspectives

Many efforts have been made to produce artificial materials with biomimetic properties for applications in binding assays. Among these efforts, the technique of molecular imprinting has received much attention because of the high selectivity obtainable for molecules of interest, robustness of the produced polymers, simple and short synthesis, and excellent cost efficiency. In this review, progress in the field of molecularly imprinted sorbent assays is discussed-with a focus on work conducted from 2005 to date.

An effective way to imprint protein with the preservation of template structure by using a macromolecule as the functional monomer

A novel strategy of using a macromolecular functional monomer to stabilize and imprint protein was proposed for the first time.

Molecular docking simulations for macromolecularly imprinted polymers

Molecularly imprinted polymers are fully synthetic antibody mimics prepared via the crosslinking of organic monomers in the presence of an analyte. This general procedure is now well developed for small molecule templates; however, attempts to extend the same techniques to the macromolecular regime have achieved limited success to date. We employ molecular docking simulations to investigate the interactions between albumin, a common protein template, and frequently employed ligands used in the literature at the molecular level. Specifically, we determine the most favorable binding sites for these ligands on albumin and determine the types of non-covalent interactions taking place based on the amino acids present nearby this binding pocket. Our results show that hydrogen bonding, electrostatic interactions, and hydrophobic interactions occur between amino acids side chains and ligands. Several interactions are also taking place with the polypeptide backbone, potentially disrupting the protein's secondary structure. We show that several of the ligands preferentially bind to the same sites on the protein, which indicates that if multiple monomers are used during synthesis then competition for the same amino acids could lead to non-specific recognition. Both of these results provide rational explanations for the lack of success to date in the field.