Probing Ligand Binding Sites on Large Proteins by Nuclear Magnetic Resonance Spectroscopy of Genetically Encoded Non-Canonical Amino Acids

N6-(((trimethylsilyl)-methoxy)carbonyl)-l-lysine (TMSK) and N6-trifluoroacetyl-l-lysine (TFAK) are non-canonical amino acids, which can be installed in proteins by genetic encoding. In addition, we describe a new aminoacyl-tRNA synthetase specific for N6-(((trimethylsilyl)methyl)-carbamoyl)-l-lysine (TMSNK), which is chemically more stable than TMSK. Using the dimeric SARS-CoV-2 main protease (Mpro) as a model system with three different ligands, we show that the 1H and 19F nuclei of the solvent-exposed trimethylsilyl and CF3 groups produce intense signals in the nuclear magnetic resonance (NMR) spectrum. Their response to active-site ligands differed significantly when positioned near rather than far from the active site. Conversely, the NMR probes failed to confirm the previously reported binding site of the ligand pelitinib, which was found to enhance the activity of Mpro by promoting the formation of the enzymatically active dimer. In summary, the amino acids TMSK, TMSNK, and TFAK open an attractive path for site-specific NMR analysis of ligand binding to large proteins of limited stability and at low concentrations.

Antiviral cyclic peptides targeting the main protease of SARS-CoV-2

Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (M^pro) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 M^pro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of M^pro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these M^pro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC₅₀ values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.

RaPID mRNA display was used for the discovery of antiviral cyclic peptides that potently and selectively inhibit SARS-CoV-2 M^pro. The most potent inhibitor exhibited a novel binding mode, interacting with residues across the homodimer interface.

Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming

The contact system comprises a series of serine proteases that mediate procoagulant and proinflammatory activities via the intrinsic pathway of coagulation and the kallikrein-kinin system, respectively. Inhibition of Factor XIIa (FXIIa), an initiator of the contact system, has been demonstrated to lead to thrombo-protection and anti-inflammatory effects in animal models and serves as a potentially safer target for the development of antithrombotics. Herein, we describe the use of the Randomised Nonstandard Peptide Integrated Discovery (RaPID) mRNA display technology to identify a series of potent and selective cyclic peptide inhibitors of FXIIa. Cyclic peptides were evaluated in vitro, and three lead compounds exhibited significant prolongation of aPTT, a reduction in thrombin generation, and an inhibition of bradykinin formation. We also describe our efforts to identify the critical residues for binding FXIIa through alanine scanning, analogue generation, and via in silico methods to predict the binding mode of our lead cyclic peptide inhibitors.

Inhibition of ionizing radiation recovery processes in polyamine-depleted Chinese hamster cells

Polyamines are involved in many cellular processes, including DNA structure and function. Since DNA, or some DNA-containing structure, is known to be the target for cell killing induced by ionizing radiation and a number of chemotherapeutic agents, we investigated the effects of polyamine depletion on cytotoxic responses of Chinese hamster cells to X-irradiation. Colony forming ability after single, acute radiation exposures of cells growing under oxic conditions was minimally affected by endogenous putrescine and spermidine depletion, achieved after treatment with alpha-difluoromethylornithine. Survival of cells rendered hypoxic and then irradiated was unaffected by alpha-difluoromethylornithine treatment. However, cellular recovery processes were nearly completely suppressed in polyamine-depleted cells, including sublethal damage recovery, as evidenced by split-dose irradiations in log phase cultures, and potentially lethal damage recovery, observed when growth-inhibited cultures were allowed time to repair radiation damage prior to being plated for colony formation. Both these recovery processes were restored by exogenous putrescine treatment. Reaccumulation of intracellular spermidine content closely correlated with restoration of potentially lethal damage recovery. Depletion of putrescine and spermidine pools had little effect on either single or double strand DNA break production or rejoining. These data demonstrate that both sublethal and potentially lethal damage recovery are polyamine-dependent processes in Chinese hamster cells, and imply that the mechanisms by which hamster cells recovery from these types of radiation damage are unrelated to their ability to rejoin DNA strand breaks, at least during the first hour after irradiation. Finally, these results suggest that the depletion of tumor polyamine content may be an effective method of enhancing the sensitivity of human tumors to fractionated radiotherapy.

An in vitro clonal assay for bladder cancer: studies of the biologic potential of the urothelium and determination of in vitro sensitivity to cytotoxic agents

We have applied an in vitro colony-forming assay system to the study of primary urothelial explants obtained transurethrally by bladder barbotage and tumor biopsy from 91 patients. Urothelial cells obtained by bladder barbotage from patients with bladder cancer and from a "control" group of individuals exhibit differential capacity to clone in agar. Of samples from bladder cancer patients, 88% formed colonies, whereas only 27% of these from a "control" group did so. Of samples from a "suspicious" patient group, 70% formed colonies. In vitro drug sensitivity studies of cells obtained by biopsy of solid tumors demonstrate a spectrum of drug sensitivity to cytotoxic agents.

Effect of host-cell interactions on clonogenic carcinoma cells in human malignant effusions

We have studied the clonogenic capacity of tumour cells in agar from 38 malignant effusions from 31 patients with epithelial tumours. Colony formation of unfractionated cells, varies considerably from patient to patient, and is positively correlated with the percentage of tumour cells in the sample. Clonogenicity was shown to be reduced in 8/9 cases by removal of plastic-adherent and iron-phagocytic cells. In the ninth case, increased clonogenicity occurred after this procedure. When the autologous adherent cells were removed from the effusion and used in reconstitution experiments as an underlayer in a two-layer agar system, they were able to reverse the effect of the initial fractionation in a dose-dependent fashion. This indicates cellular communication based on release of a diffusible product of plastic-adherent cells. Morphological, phagocytic and prostaglandin-synthetic analysis of the fractions involved in the reconstitution experiments implicate the macrophage as the operative cell in this interaction. However, an accessory role for lymphoid cells or tumour cells themselves cannot be excluded.

Application of in vitro soft agar techniques for growth of tumor cells to the study of colon cancer

An in vitro assay to measure the clonogenic or colony-forming capability of cancer cells present in biopsy samples has recently been applied to study the biology and drug-sensitivity of a variety of human neoplasms. This approach appears to be suitable for study of the tumor stem or progenitor cells present in malignant effusions from patients with colonic carcinoma. In our preliminary studies, morphology of the tumor colonies by inverted microscopy and with Papanicolaou staining of dried agar plating layers as well as immunofluorescent localization with a specific antiserum to human carcinoembrionic antigen have been used as markers of the neoplastic origin of colon tumor colony-forming cells. Successful application of this assay to colonic solid tumors will require improvement in techniques for disaggregation of viable clonogenic cells. We anticipate that short term clonal assays will have increasing use for clinical and biological studies of human colon cancer.

Development of an agar-methyl cellulose clonogenic assay for cells in transitional cell carcinoma of the human bladder

We report the development of a clonogenic assay for progenitor cells in transitional cell carcinoma of the bladder. Colony growth has been demonstrated from cells obtained both from surgical biopsies and from bladder barbotages. Electron microscopic and karyotypic evidence supports the contention that these progenitors represent a part of the population maintaining the tumor in vivo. Colony growth occurred in 9 of 11 surgical biopsy samples and in 6 of 6 bladder barbotage samples. Plating efficiency ranged up to 0.7%, and colony size was in some instances greater than 1000 cells. The assay appears potentially useful for analysis of the biology of human transitional cell carcinoma.

Stimulation of recombination in phage T4 by nitrous acid-induced lesions

Recombination of phage T4 can be stimulated more than sixfold above the spontaneous level by treatment with nitrous acid, indicating that the lesions induced by this agent are strongly recombinogenic. Two temperature sensitive mutants defective in exonuclease functions showed less than the wild-type spontaneous level of recombination even after nitrous acid treatment and a ligase mutant showed a highly elevated frequency of recombination after treatment. Since these same mutants have analogous effects on spontaneous recombination, the results imply that nitrous acid-induced lesions in DNA stimulate a recombinational repair process similar in some of its enzymic steps to spontaneous recombination.