Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also passive membrane permeability. As "journey" through membranes cannot be monitored experimentally, little is known about underlying process, which hinders rational design. Here, we use molecular simulations uncover how cyclic permeate a membrane. We show that side chains can act as "molecular anchors", establishing first contact with enabling...

Advances in structural biology and the exponential increase amount of high-quality experimental data available Protein Data Bank has motivated numerous studies to tackle grand challenge predicting protein structures. In 2020 AlphaFold2 revolutionized field using a combination artificial intelligence evolutionary information contained multiple sequence alignments. Antibodies are one most important classes biotherapeutic proteins. Accurate structure models prerequisite advance biophysical...

Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes atomistic detail, including and unfolding processes of proteins. However, the accuracy ensembles derived from MD inevitably relies on quality underlying force field combination with respective water model. Here, we investigate protein folding, unfolding, misfolding fast-folding proteins by examining different fields their...

While antibody-based therapeutics have grown to be one of the major classes novel medicines, some antibody development candidates face significant challenges regarding expression levels, solubility, as well stability and aggregation, under physiological storage conditions. A determinant those properties is surface hydrophobicity, which promotes unspecific interactions has repeatedly proven problematic in drugs. Multiple computational methods been devised for in-silico prediction often using...

Abstract In the last decades, antibodies have emerged as one of most important and successful classes biopharmaceuticals. The highest variability diversity an antibody is concentrated on six hypervariable loops, also known complementarity determining regions (CDRs) shaping antigen-binding site, paratope. Whereas it was assumed that certain sequences can only adopt a limited set backbone conformations, in this study we present kinetic classification several paratope states solution. Using...

Solvation and hydrophobicity play a key role in variety of biological mechanisms. In substrate binding, but also structure-based drug design, the thermodynamic properties water molecules surrounding given protein are high interest. One main algorithms devised recent years to quantify is grid inhomogeneous solvation theory (GIST), which calculates these features on protein. Despite inherent advantages GIST, computational demand major drawback, as calculations for larger systems can take days...

During the affinity maturation process immune system produces antibodies with higher specificity and activity through various rounds of somatic hypermutations in response to an antigen. Elucidating is fundamental understanding immunity development biotherapeutics. Therefore, we analyzed 10 pairs antibody fragments differing their distinct stages using metadynamics combination molecular dynamics (MD) simulations. We investigated differences flexibility CDR-H3 loop global changes plasticity...

Biomolecular recognition between proteins follows complex mechanisms, the understanding of which can substantially advance drug discovery efforts. Here, we track each step binding process in atomistic detail with molecular dynamics simulations using trypsin and its inhibitor bovine pancreatic (BPTI) as a model system. We use umbrella sampling to cover range unbinding pathways. Starting from these simulations, subsequently seed classical at different stages combine them Markov state model....

Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. observed enthalpic and entropic differences between ice-binding sites inactive surface reveal key properties essential for proteins order bind ice: While contributions are similar all...

A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation exposure hydrophobic surface regions solvent. Many current techniques predict relative propensity antibodies via precalculated scales hydrophobicity or single amino acids. However, those cannot describe nonadditive effects a residue's surrounding on its hydrophobicity. Therefore, they are inherently limited ability impact subtle differences molecular structure...

The electrostatic properties of proteins arise from the number and distribution polar charged residues. Electrostatic interactions in play a critical role numerous processes such as molecular recognition, protein solubility, viscosity, antibody developability. Thus, characterizing quantifying are prerequisites for understanding these processes. Here, we present PEP-Patch, tool to visualize quantify potential on surface terms patches, denoting separated areas with common physical property. We...

Sharks and other cartilaginous fish produce new antigen receptor (IgNAR) antibodies, as key part of their humoral immune response are the phylogenetically oldest living organisms that possess an immunoglobulin (Ig)-based adaptive system. IgNAR antibodies naturally occurring heavy-chain-only recognize antigens with single domain variable regions (VNARs). In this study, we structurally biophysically elucidate effect antibody humanization a previously published spiny dogfish VNAR (parent E06),...

Abstract Antibodies have the ability to bind various types of antigens and recognize different antibody-binding sites (epitopes) same antigen with binding affinities. Due conserved structural framework antibodies, their specificity is mainly determined by antigen-binding site (paratope). Therefore, characterization epitopes in combination describing involved conformational changes paratope upon crucial understanding predicting antibody-antigen binding. Using molecular dynamics simulations...

Fab consist of a heavy and light chain can be subdivided into variable (V H V L ) constant region (C 1 C ). The contains the complementarity-determining (CDR), which is formed by six hypervariable loops, shaping antigen binding site, paratope. Apart from CDR both elbow angle relative interdomain orientations –V 1–C domains influence shape Thus, characterization interface dynamics essential to specificity. We studied nine antigen-binding fragments (Fab) investigate affinity maturation,...

The relation of surface polarity and conformational preferences is decisive for cell permeability thus bioavailability macrocyclic drugs. Here, we employ grid inhomogeneous solvation theory (GIST) to calculate free energies a series six macrocycles in water chloroform as measure passive membrane permeability. We perform accelerated molecular dynamics simulations capture diverse structural ensemble chloroform, allowing direct profiling solvent-dependent preferences. Subsequent GIST...

Reliable information on partition coefficients plays a key role in drug development, as solubility decisively affects bioavailability. In physicochemical context, the coefficient of solute between two different solvents can be described function solvation free energies. Hence, substantial scientific efforts have been made toward accurate predictions energies various solvents. The grid inhomogeneous theory (GIST) facilitates calculation this study, we introduce an extended version GIST...

Macrocycles are a promising class of compounds as therapeutics for difficult drug targets due to favorable combination properties: They often exhibit improved binding affinity compared their linear counterparts reduced conformational flexibility, while still being able adapt environments different polarity. To assist in the rational design macrocyclic drugs, there is need computational methods that can accurately predict ensembles macrocycles environments. Molecular dynamics (MD) simulations...

Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist predict solvation of compounds small molecules large biomolecules. Arguably most precise are those based on molecular dynamics (MD) simulations explicit solvent. One theory that has seen increased use is inhomogeneous (IST). However, while many applications require accurate description salt-water mixtures, no implementation IST currently able...

Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information enhance structure-based binding predictions. We recently extended GIST toward chloroform as solvent allow the prediction passive membrane permeability. Here, we further generalize algorithm all solvents that can be modeled rigid molecules. This restriction is inherent method and already present in inhomogeneous...

Abstract Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations investigate melting process 16 antigen binding fragments (Fabs). We describe Fab dissociation mechanisms, showing a separation in V H –V L C 1–C domains. found...

We evaluated a workflow to reliably sample the conformational space of set 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations overcome high energy barriers, in particular, cis–trans isomerization peptide bonds. find that our approach performs very well polar solvents like water and dimethyl sulfoxide. Interestingly, protonation state secondary amine ring only slightly influences ensembles test systems. For several macrocycles, determining...

Abstract In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination high specificity with long serum half‐life and low risk side‐effects. Diabodies are popular novel antibody format, consisting two F v domains connected short linkers. Like IgG antibodies, they simultaneously bind target proteins. However, offer altered properties, given smaller size higher rigidity. this study, we conducted the—to our knowledge—first molecular dynamics (MD)...

The family of profilin allergens is a common class proteins found in plants, viruses and various eukaryotes including mammals. Profilins are characterized by an evolutionary conserved structural fold, which responsible for their cross-reactive nature Immunoglobulin E (IgE) antibodies. Despite high overall similarity, they exhibit substantial differences biophysical properties, such as thermal pH stability. To understand the origin these functional Amb 8, Art v 4 Bet 2, we performed constant...

ABSTRACT The electrostatic properties of proteins arise from the number and distribution polar charged residues. Due to their long-ranged nature, interactions in play a critical role numerous processes, such as molecular recognition, protein solubility, viscosity, antibody developability. Thus, characterizing quantifying is pre-requisite for understanding these processes. Here, we present PEP-Patch, tool visualize quantify potential on surface showcase its applicability elucidate protease...