Ordered immobilization of serine proteases enabled by a linchpin directed modification platform.

We report a chemoselective and site-selective precision engineering of lysine in proteases. The mild and physiological reaction conditions keep their auto-degradation under control. Furthermore, it enables single-site ordered immobilization, enhancing protein digestion and peptide mapping efficiency.

Discovery of a Tunable Heterocyclic Electrophile 4-Chloro-pyrazolopyridine That Defines a Unique Subset of Ligandable Cysteines.

Electrophilic small molecules with novel reactivity are powerful tools that enable activity-based protein profiling and covalent inhibitor discovery. Here, we report a reactive heterocyclic scaffold, 4-chloro-pyrazolopyridine (CPzP) for selective modification of proteins via a nucleophilic aromatic substitution (SNAr) mechanism. Chemoproteomic profiling reveals that CPzPs engage cysteines within functionally diverse protein sites including ribosomal protein S5 (RPS5), inosine monophosphate dehydrogenase 2 (IMPDH2), and heat shock protein 60 (HSP60). Through the optimization of appended recognition elements, we demonstrate the utility of CPzP for covalent inhibition of prolyl endopeptidase (PREP) by targeting a noncatalytic active-site cysteine. This study suggests that the proteome reactivity of CPzPs can be modulated by both electronic and steric features of the ring system, providing a new tunable electrophile for applications in chemoproteomics and covalent inhibitor design.

Competitive Charge Separation Pathways in a Flexible Molecular Folda-Dimer.

We report the photophysical properties of a molecular folda-dimer system PDI-AnEt2-PDI, where the electron-donating N,N-diethylaniline (AnEt2) moiety bridges two electron-accepting perylene diimide (PDI) chromophores. The conformationally flexible PDI-AnEt2-PDI adopts either an open (two PDIs far apart) or folded (two PDIs within π-stacking distance) conformation, depending on the solvent environment. We characterized the photoinduced charge separation dynamics of both open and folded forms in solvents of varying polarity. The open form undergoes charge separation to give PDI•--AnEt2•+-PDI (Bridge electron transfer) independent of solvent polarity. The folded form exhibits two charge separation photoproducts, yielding both PDI•--AnEt2•+-PDI and PDI•--AnEt2-PDI•+, the latter of which is formed via symmetry-breaking charge separation (SBCS) between the two π-stacked PDI chromophores. Our results further indicate that the conformational flexibility of the folda-dimer leads to unexpected excimer formation in some open form conditions. In contrast, no excimer formation is observed in the folded form, indicating that this geometry preferentially yields the SBCS instead. Our results provide insight into how conformationally flexible folda-dimer systems can be designed and built to tune competitive photophysical pathways.

Human Behavior-Inspired Linchpin-Directed Catalysis for Traceless Precision Labeling of Lysine in Native Proteins.

The complex social ecosystem regulates the spectrum of human behavior. However, it becomes relatively easier to understand if we disintegrate the contributing factors, such as locality and interacting partners. Interestingly, it draws remarkable similarity with the behavior of a residue placed in a social setup of functional groups in a protein. Can it inspire principles for creating a unique environment for the precision engineering of proteins? We demonstrate that localization-regulated interacting partner(s) could render precise and traceless single-site modification of structurally diverse native proteins. The method targets a combination of high-frequency Lys residues through an array of reversible and irreversible reactions. However, excellent simultaneous control over chemoselectivity, site selectivity, and modularity ensures that the user-friendly protocol renders acyl group installation, including post-translational modifications (PTMs), on a single Lys. Besides, it offers a chemically orthogonal handle for the installation of probes. Also, a purification protocol integration delivers analytically pure single-site tagged protein bioconjugates. The precise labeling of a surface Lys residue ensures that the structure and enzymatic activities remain conserved post-bioconjugation. For example, the precise modification of insulin does not affect its uptake and downstream signaling pathway. Further, the method enables the synthesis of homogeneous antibody-fluorophore and antibody-drug conjugates (AFC and ADC; K183 and K249 labeling). The trastuzumab-rhodamine B conjugate displays excellent serum stability along with antigen-specific cellular imaging. Further, the trastuzumab-emtansine conjugate offers highly specific antiproliferative activity toward HER-2 positive SKBR-3 breast cancer cells. This work validates that disintegrate theory can create a comprehensive platform to enrich the chemical toolbox to meet the technological demands at the chemistry, biology, and medicine interface.

Reactivity and Selectivity Principles in Native Protein Bioconjugation.

Are chemical methods capable of precisely engineering the native proteins? Is it possible to develop platforms that can empower the regulation of chemoselectivity, site-selectivity, modularity, protein-specificity, and site-specificity? This account delineates our research journey in the last ten years on the developments revolving around these questions. It will range from the realization of chemoselective and site-selective labeling of reactivity hotspots to modular linchpin directed modification (LDM®) platform and site-specific Gly-tag® technology. Also, we outline a few biotechnology tools, including Maspecter®, that accelerated the detailed analysis of the bioconjugates and rendered a powerful toolbox for homogeneous antibody-drug conjugates (ADCs).

Linchpins empower promiscuous electrophiles to enable site-selective modification of histidine and aspartic acid in proteins.

The conservation of chemoselectivity becomes invalid for multiple electrophilic warheads during protein bioconjugation. Consequently, it leads to unpredictable heterogeneous labeling of proteins. Here, we report that a linchpin can create a unique chemical space to enable site-selectivity for histidine and aspartic acid modifications overcoming the pre-requisite of chemoselectivity.

Insight into Electron Transfer from a Redox Polymer to a Photoactive Protein.

Biohybrid photoelectrochemical systems in photovoltaic or biosensor applications have gained considerable attention in recent years. While the photoactive proteins engaged in such systems usually maintain an internal charge separation quantum yield of nearly 100%, the subsequent steps of electron and hole transfer beyond the protein often limit the overall system efficiency and their kinetics remain largely uncharacterized. To reveal the dynamics of one of such charge-transfer reactions, we report on the reduction of Rhodobacter sphaeroides reaction centers (RCs) by Os-complex-modified redox polymers (P-Os) characterized using transient absorption spectroscopy. RCs and P-Os were mixed in buffered solution in different molar ratios in the presence of a water-soluble quinone as an electron acceptor. Electron transfer from P-Os to the photoexcited RCs could be described by a three-exponential function, the fastest lifetime of which was on the order of a few microseconds, which is a few orders of magnitude faster than the internal charge recombination of RCs with fully separated charge. This was similar to the lifetime for the reduction of RCs by their natural electron donor, cytochrome c2. The rate of electron donation increased with increasing ratio of polymer to protein concentrations. It is proposed that P-Os and RCs engage in electrostatic interactions to form complexes, the sizes of which depend on the polymer-to-protein ratio. Our findings throw light on the processes within hydrogel-based biophotovoltaic devices and will inform the future design of materials optimally suited for this application.

Chemoselective and Site-Selective Lysine-Directed Lysine Modification Enables Single-Site Labeling of Native Proteins.

The necessity for precision labeling of proteins emerged during the efforts to understand and regulate their structure and function. It demands selective attachment of tags such as affinity probes, fluorophores, and potent cytotoxins. Here, we report a method that enables single-site labeling of a high-frequency Lys residue in the native proteins. At first, the enabling reagent forms stabilized imines with multiple solvent-accessible Lys residues chemoselectively. These linchpins create the opportunity to regulate the position of a second Lys-selective electrophile connected by a spacer. Consequently, it enables the irreversible single-site labeling of a Lys residue independent of its place in the reactivity order. The user-friendly protocol involves a series of steps to deconvolute and address chemoselectivity, site-selectivity, and modularity. Also, it delivers ordered immobilization and analytically pure probe-tagged proteins. Besides, the methodology provides access to antibody-drug conjugate (ADC), which exhibits highly selective anti-proliferative activity towards HER-2 expressing SKBR-3 breast cancer cells.

Highlights of Indian Council of Medical Research National Ethical Guidelines for Biomedical and Health Research Involving Human Participants.

Advancements in the field of biomedical and health research pose new ethical challenges warranting the need for constant updation in the existing ethics guidance. Realizing this, revision of "Ethical Guidelines for Biomedical Research on Human Participants (2006)" was initiated in the year 2015. The preparation of guidelines was a participatory process involving large number of stakeholders from various backgrounds in order to get a variety of perspectives. The initial draft went through an extensive process of consultation at both regional and national level, with experts and stakeholders from academia, govt. agencies, departments and ministries, public and private institutions, pharmaceutical industry, non-governmental organizations, patient organizations, regulators, international agencies as well as with public. The revised "National Ethical Guidelines for Biomedical and Health Research Involving Human Participants, 2017" were released on October 12, 2017, and address ethical concerns, in accordance to the sociocultural milieu of our country. New sections have been added on informed consent process, vulnerability, biological materials, biobanking and datasets, responsible conduct of research, sociobehavioral research, research in emergencies or disasters. The revised guidelines must be followed by all stakeholders who are engaged in biomedical and health research including sponsors, institutions, ethics committees, and researchers. It is expected that the implementation of these guidelines would help to protect the dignity, rights, safety and well-being of research participants and also to improve the quality of biomedical and health research.

"Simple Methods to Derive Primary Malignant Glioma Cell Lines and Assay of Cellular Damage for Preclinical Studies".

Primary malignant glioma cell lines are being used for initial screening of anticancer agents. We utilized a simple mechanical disaggregation method for deriving cell lines from tumor tissues; and a Coverslip Culture-Acridine Orange Staining method to study cellular damage. Cell lines could be grown for up to three passages within three weeks after surgery. Cell proliferation, total cellular damage, and MTT assay were studied as parameters of cytotoxic response. Frequencies of damaged cells varied in different cell lines; and increased after cytotoxic treatments under clinically relevant conditions. These methods could contribute to preclinical evaluation of treatment response before commencement of radio-chemotherapy.