Kabirul Islam

Expanding cofactor repertoire of protein lysine methyltransferase for substrate labeling.

Protein lysine methyltransferases (PKMTs) play crucial roles in normal physiology and disease processes. Profiling PKMT targets is an important but challenging task. With cancer-relevant G9a as a target, we have demonstrated success in developing S-adenosyl-L-methionine (SAM) analogues, particularly (E)-hex-2-en-5-ynyl SAM (Hey-SAM), as cofactors for engineered G9a. Hey-SAM analogue in combination with G9a Y1154A mutant modifies the same set of substrates as their native counterparts with remarkable efficiency. (E)-Hex-2-en-5-ynylated substrates undergo smooth click reaction with an azide-based probe. This approach is thus suitable for substrate characterization of G9a and expected to further serve as a starting point to evolve other PKMTs to utilize a similar set of cofactors.

Bioorthogonal profiling of protein methylation using azido derivative of S-adenosyl-L-methionine.

Protein methyltransferases (PMTs) play critical roles in multiple biological processes. Because PMTs often function in vivo through forming multimeric protein complexes, dissecting their activities in the native contexts is challenging but relevant. To address such a need, we envisioned a Bioorthogonal Profiling of Protein Methylation (BPPM) technology, in which a SAM analogue cofactor can be utilized by multiple rationally engineered PMTs to label substrates of the corresponding native PMTs. Here, 4-azidobut-2-enyl derivative of S-adenosyl-L-methionine (Ab-SAM) was reported as a suitable BPPM cofactor. The resultant cofactor-enzyme pairs were implemented to label specifically the substrates of closely related PMTs (e.g., EuHMT1 and EuHMT2) in a complex cellular mixture. The BPPM approach, coupled with mass spectrometric analysis, enables the identification of the nonhistone targets of EuHMT1/2. Comparison of EuHMT1/2s methylomes indicates that the two human PMTs, although similar in terms of their primary sequences, can act on the distinct sets of nonhistone targets. Given the conserved active sites of PMTs, Ab-SAM and its use in BPPM are expected to be transferable to other PMTs for target identification.

Profiling Genome-Wide Chromatin Methylation with Engineered Posttranslation Apparatus within Living Cells

Protein methyltransferases (PMTs) have emerged as important epigenetic regulators in myriad biological processes in both normal physiology and disease conditions. However, elucidating PMT-regulated epigenetic processes has been hampered by ambiguous knowledge about in vivo activities of individual PMTs particularly because of their overlapping but nonredundant functions. To address limitations of conventional approaches in mapping chromatin modification of specific PMTs, we have engineered the chromatin-modifying apparatus and formulated a novel technology, termed clickable chromatin enrichment with parallel DNA sequencing (CliEn-seq), to probe genome-wide chromatin modification within living cells. The three-step approach of CliEn-seq involves in vivo synthesis of S-adenosyl-L-methionine (SAM) analogues from cell-permeable methionine analogues by engineered SAM synthetase (methionine adenosyltransferase or MAT), in situ chromatin modification by engineered PMTs, subsequent enrichment and sequencing of the uniquely modified chromatins. Given critical roles of the chromatin-modifying enzymes in epigenetics and structural similarity among many PMTs, we envision that the CliEn-seq technology is generally applicable in deciphering chromatin methylation events of individual PMTs in diverse biological settings.

Se-adenosyl-L-selenomethionine cofactor analogue as a reporter of protein methylation.

Posttranslational methylation by S-adenosyl-L-methionine(SAM)-dependent methyltransferases plays essential roles in modulating protein function in both normal and disease states. As such, there is a growing need to develop chemical reporters to examine the physiological and pathological roles of protein methyltransferases. Several sterically bulky SAM analogues have previously been used to label substrates of specific protein methyltransferases. However, broad application of these compounds has been limited by their general incompatibility with native enzymes. Here we report a SAM surrogate, ProSeAM (propargylic Se-adenosyl-l-selenomethionine), as a reporter of methyltransferases. ProSeAM can be processed by multiple protein methyltransferases for substrate labeling. In contrast, sulfur-based propargylic SAM undergoes rapid decomposition at physiological pH, likely via an allene intermediate. In conjunction with fluorescent/affinity-based azide probes, copper-catalyzed azide-alkyne cycloaddition chemistry, in-gel fluorescence visualization and proteomic analysis, we further demonstrated ProSeAMs utility to profile substrates of endogenous methyltransferases in diverse cellular contexts. These results thus feature ProSeAM as a convenient probe to study the activities of endogenous protein methyltransferases.

Total synthesis of the novel angiogenesis inhibitors epoxyquinols A and B

The synthesis of the recently discovered angiogenesis inhibitors epoxyquinols A and B, having novel polyketide derived dimeric structures, has been accomplished from the readily available Diels–Alder adduct of cyclopentadiene and p-benzoquinone through a short, simple and flexible strategy that is diversity oriented and can be adapted to an asymmetric variant.

Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation

Significance Many proteins undergo various posttranslational modifications for proper functions. One such modification is methylation carried out by enzyme–cofactor pairs of protein methyltransferases (PMTs) and S-adenosyl-L-methionine (SAM). Identification of methylated proteins is quite challenging because of the small size and chemical inertness of the methyl group. To address this challenge, we have synthesized SAM surrogates by replacing SAM’s methyl group with bulky, chemically active functionalities and demonstrated their utility as alternative cofactors of engineered PMTs for substrate labeling. Proteins modified with such chemical moieties are amenable to bioorthogonal reactions for subsequent enrichment and identification. An engineered enzyme–cofactor pair has been successfully used to reveal numerous methylated proteins. Protein methyltransferase (PMT)-mediated posttranslational modification of histone and nonhistone substrates modulates stability, localization, and interacting partners of target proteins in diverse cellular contexts. These events play critical roles in normal biological processes and are frequently deregulated in human diseases. In the course of identifying substrates of individual PMTs, bioorthogonal profiling of protein methylation (BPPM) has demonstrated its merits. In this approach, specific PMTs are engineered to process S-adenosyl-L-methionine (SAM) analogs as cofactor surrogates and label their substrates with distinct chemical modifications for target elucidation. Despite the proof-of-concept advancement of BPPM, few efforts have been made to explore its generality. With two cancer-relevant PMTs, EuHMT1 (GLP1/KMT1D) and EuHMT2 (G9a/KMT1C), as models, we defined the key structural features of engineered PMTs and matched SAM analogs that can render the orthogonal enzyme–cofactor pairs for efficient catalysis. Here we have demonstrated that the presence of sulfonium-β-sp2 carbon and flexible, medium-sized sulfonium-δ-substituents are crucial for SAM analogs as BPPM reagents. The bulky cofactors can be accommodated by tailoring the conserved Y1211/Y1154 residues and nearby hydrophobic cavities of EuHMT1/2. Profiling proteome-wide substrates with BPPM allowed identification of >500 targets of EuHMT1/2 with representative targets validated using native EuHMT1/2 and SAM. This finding indicates that EuHMT1/2 may regulate many cellular events previously unrecognized to be modulated by methylation. The present work, therefore, paves the way to a broader application of the BPPM technology to profile methylomes of diverse PMTs and elucidate their downstream functions.

Total Synthesis of (±)‐Otteliones A and B

The biologically potent antitubercular and anticancer otteliones A and B (see scheme) have been synthesized from readily available starting materials by using a short, simple, efficient, and flexible strategy. The structural ambiguity of the natural products has been resolved.

Enantioselective total syntheses of (+)- and (-)-ottelione A and (+)- and (-)-ottelione B. Absolute configuration of the novel, biologically active natural products

Following our recent total synthesis of the biologically potent natural products otteliones A and B in racemic form, we have now accomplished the total synthesis of both the enantiomers of otteliones A and B through an enantiodivergent strategy emanating from the readily available Diels-Alder adduct of cyclopentadiene and p-benzoquinone. These endeavors have led to the elucidation of the absolute configuration of naturally occurring otteliones A and B.

Allele-Specific Chemical Genetics: Concept, Strategies, and Applications

The relationship between DNA and protein sequences is well understood, yet because the members of a protein family/subfamily often carry out the same biochemical reaction, elucidating their individual role in cellular processes presents a challenge. Forward and reverse genetics have traditionally been employed to understand protein functions with considerable success. A fundamentally different approach that has gained widespread application is the use of small organic molecules, known as chemical genetics. However, the slow time-scale of genetics and inherent lack of specificity of small molecules used in chemical genetics have limited the applicability of these methods in deconvoluting the role of individual proteins involved in fast, dynamic biological events. Combining the advantages of both the techniques, the specificity achieved with genetics along with the reversibility and tunability of chemical genetics, has led to the development of a powerful approach to uncover protein functions in complex biological processes. This technique is known as allele-specific chemical genetics and is rapidly becoming an essential toolkit to shed light on proteins and their mechanism of action. The current review attempts to provide a comprehensive description of this approach by discussing the underlying principles, strategies, and successful case studies. Potential future implications of this technology in expanding the frontiers of modern biology are discussed.

Face-selectivity in [4+2]-cycloadditions to novel polycyclic benzoquinones. Remarkable stereodirecting effects of a remote cyclopropane ring and an olefinic bond

Pi-Face selectivity in Diels–Alder reactions between specially crafted bicyclo[2.2.2]octane-fused benzoquinones, where the dienophilic moiety is imbedded in an isosteric environment, can be modulated by a remote olefinic bond and a cyclopropane ring. Quantum mechanical calculations while reproducing the observed diastereoselectivities at the TS level indicate the involvement of ground state orbital effects.