Cancer immunotherapy has attracted increasing attention over the last few years. Programmed cell death protein 1 (PD-1) promotes self-tolerance and inhibits immune responses by modulating the T-cell function. The interaction between PD-1 and programmed cell death ligand-1 (PD-L1) leads to immune exhaustion, protecting cancer cells from destruction. Here, we computationally designed a novel ligand named 1508 that binds to an unprecedented PD-1 cavity identified by MixMD and defined by amino acid residues Lys78 to Val97. We showed through a set of MD simulations totaling 12.5 μs that ligand 1508 establishes frequent cation−π and hydrogen bonding interactions with amino acid residues Lys78 and Arg86, respectively, and stabilizes the PD-1 C′D loop in a conformation that does not favor PD-1−PD-L1 complex formation. This study highlights the power of MixMD in exposing new cavities prone to protein−protein complex inhibition and establishes the basis for the design of new molecules that target the PD-1 C′D cavity as an alternative for exploring the modulation of the PD-1−PD-L1 complex in cancer therapy.

Integrins are transmembrane receptors that play a critical role in many biological processes which can be therapeutically modulated using integrin blockers, such as peptidomimetic ligands. This work aimed to develop new potential β1 integrin antagonists using modeled receptors based on the aligned crystallographic structures and docked with three lead compounds (BIO1211, BIO5192, and TCS2314), widely known as α4β1 antagonists. Lead-compound complex optimization was performed by keeping intact the carboxylate moiety of the ligand, adding substituents in two other regions of the molecule to increase the affinity with the target. Additionally, pharmacokinetic predictions were performed for the ten best ligands generated, with the lowest docking interaction energy obtained for α4β1 and BIO5192. Results revealed an essential salt bridge between the BIO5192 carboxylate group and the Mg2+ MIDAS ion of the integrin. We then generated more than 200 new BIO5192 derivatives, some with a greater predicted affinity to α4β1. Furthermore, the significance of retaining the pyrrolidine core of the ligand and increasing the therapeutic potential of the new compounds is emphasized. Finally, one novel molecule (1592) was identified as a potential drug candidate, with appropriate pharmacokinetic profiles, similar dynamic behavior at the integrin interaction site compared with BIO5192, and a higher predicted affinity to VLA-4.

Flavonoids are a class of natural products widely available in medicinal and dietary plants. Their pharmacological use has shown the potential to reduce the risk of different types of cancer, among other prevalent diseases. Their molecular scaffold inhibits the PD-1/PD-L1 axis, an important pathway related to the adaptive immune resistance of cancer cells already targeted for developing new cancer immunotherapy. However, despite the availability of kinetic and thermodynamic experimental data on the flavonoid–PD-1/PD-L1 interaction, there is still a lack of reliable information about their binding mode at the atomic level. Thus, we aimed to computationally predict the binding mode of flavonoid molecules with PD-1 and/or PD-L1 proteins using unbiased computational methodologies such as blind docking and supervised molecular dynamics simulation. The molecular interactions and dynamics of these predicted poses of protein-flavonoid complexes were further analyzed through multiple molecular dynamics simulations. This information, corroborated with the IC50 and KD values from available literature, was used to perform molecular matched-pair analysis to comprehensively describe the main interactions governing the inhibition of the complex PD-1/PD-L1 by the flavonoid scaffold. By analyzing the effect of substitutions in such a scaffold, we observed a clear correspondence with literature binding assays. Thus, we propose, for dimeric PD-L1, that the 7-O-glucoside forces the molecule displacement in the dimer interface. Furthermore, the 3-OH plays an essential role in stabilizing the buried binding mode by water-bridged hydrogen bonds with Asp122 and Gln66 in both extremities of the pocket. In PD-1, we suggest that flavonoids could bind through the BC loop by inducing a flip of Phe56 after a conformational change of the Asn58 glycosylation. Hence, our results introduced unprecedented information on flavonoid interaction and dynamics when complexed with PD-1 checkpoint pathway proteins and can pave the road for developing new flavonoid derivatives with selective anticancer activity.

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Introduction: Cancer is one of the leading public health problems worldwide and is among the top four causes of death in most countries. It is well established that the interaction between PD-1, an immune checkpoint receptor present in the T cell, and its ligand, PD-L1, present in cancer cells, results in immune evasion and maintenance of the tumorigenesis. Current treatments to block the interaction between PD-1 PD-L1 involve monoclonal antibodies (mAbs), such as nivolumab and pembrolizumab. Nowadays, there remains a need and interest in searching for new antibodies with better efficacy and activity.

Asthma is a chronic disease, still without a cure, and a globally significant public health problem, mainly due to continuous increase in cases. Treatment is costly due to immunosuppressive drugs mainly based on corticosteroids and beta-2 adrenergic receptor agonists. However, because of refractory cases, monoclonal antibodies usage proposed to inhibit specific molecules has become an attractive therapeutic method with promising results although expensive. The use of single domain antibodies (sdAbs), as well as camelid heavy-chain antibody variable domain (VHH), are cutting-edge biotechnological tools since they preserve the inhibition potential, specificity, sensitivity, and high-affinity but with a lower production cost and immunogenicity. Objectives:The purpose of the study is to design a model in silico of stable and specific sdAb against a pivotal pro-inflammatory cytokine involved in the allergic asthma process. Methodology:The structure of a variable heavy domain from a monoclonal antibody against this crucial pro-inflammatory cytokine, with known therapeutic effects against asthma, was used as a template to in silico build different sdAbs. Using the "camelization" approach to increase VHs solubility and stability, three specifics mutated sdAbs against this cytokine were designed. Molecular dynamics simulations of these antibodies and the wild-type VH isolated or associated with the cytokine were performed to study their predicted interaction, stability, and solubility. Results:The results for the sdAbs:cytokine complexes show that the proposed antibodies interact in a stable and long-lasting way, in addition to a broad contribution from the CDRs, that provide the interaction specificity. All mutants had higher binding free energy and hydrogen bonding scores than the wild-type, suggesting better-predicted affinity. Additionally, the chosen mutations in the sdAbs improved the stability in the mutated region and decreased the time for structure stabilization on dynamics approach. Furthermore, the predicted solubility of the mutants was higher than the wild type and similar to previously soluble nanobodies produced by our group. Conclusion:These results suggest that the proposed in silico mutations may improve the stability and solubility of these sdAbs. In addition, these mutations did not decrease the antibody ability to have a stable and long-lasting interaction with the cytokine and increased the predicted affinity, possibly contributing to the inhibitory and therapeutic effects. Nonetheless, further studies are still needed to confirm the in silico results and analyze possible side effects.

Resumo A aplicação de lipossomas para a administração controlada de fármacos tem tido um grande impacto em muitas áreas biomédicas. Verificou-se que eles são benéficos para a estabilização de compostos terapêuticos, superação de obstáculos à absorção celular e de tecidos e melhoria da biodistribuição de compostos para locais-alvo in vivo. Essa prospecção teve como objetivo analisar as patentes que tratam da utilização de lipossomas como veículos de drug delivery. A busca foi realizada nos bancos de dados do INPI e do EPO. As patentes encontradas foram analisadas quanto a quantidade, datas de publicação, país de origem dos depositantes e dos inventores, país Revista GEINTEC

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