@article {45401, title = {From a helix to a small cycle: metadynamics-inspired alpha v beta 6 integrin selective ligands}, journal = {Angewandte Chemie-International Edition}, volume = {57}, year = {2018}, month = {OCT}, pages = {14645-14649}, type = {Article}, abstract = {The RGD-recognizing alpha v beta 6 integrin has only recently emerged as a major target for cancer diagnosis and therapy. Thus, the development of selective, low-molecular-weight ligands of this receptor is still in great demand. Here, a metadynamics-driven design strategy allowed us to successfully convert a helical nonapeptide into a cyclic pentapeptide (6) showing remarkable potency and alpha v beta 6 specificity. NMR and docking studies elucidated the reasons for the high affinity and selectivity of this compound, setting the ground for the rational design of new alpha v beta 6-specific small peptides or even peptidomimetics. In vivo PET imaging studies demonstrated the potential use of 6 for medical applications.}, issn = { 1433-7851}, doi = {10.1002/anie.201803250}, author = {Di Leva, Francesco Saverio and Tomassi, Stefano and Di Maro, Salvatore and Reichart, Florian and Notni, Johannes and Dangi, Abha and Marelli, Udaya Kiran and Brancaccio, Diego and Merlino, Francesco and Wester, Hans-Juergen and Novellino, Ettore and Kessler, Horst and Marinelli, Luciana} } @article {46768, title = {EGCG impedes human Tau aggregation and interacts with Tau}, journal = {Scientific Reports}, volume = {10}, year = {2020}, month = {JUL}, pages = {12579}, type = {Article}, abstract = {

Tau aggregation and accumulation is a key event in the pathogenesis of Alzheimer{\textquoteright}s disease. Inhibition of Tau aggregation is therefore a potential therapeutic strategy to ameliorate the disease. Phytochemicals are being highlighted as potential aggregation inhibitors. Epigallocatechin-3-gallate (EGCG) is an active phytochemical of green tea that has shown its potency against various diseases including aggregation inhibition of repeat Tau. The potency of EGCG in altering the PHF assembly of full-length human Tau has not been fully explored. By various biophysical and biochemical analyses like ThS fluorescence assay, MALDI-TOF analysis and Isothermal Titration Calorimetry, we demonstrate dual effect of EGCG on aggregation inhibition and disassembly of full-length Tau and their binding affinity. The IC50 for Tau aggregation by EGCG was found to be 64.2 mu M.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-69429-6}, author = {Sonawane, Shweta Kishor and Chidambaram, Hariharakrishnan and Boral, Debjyoti and Gorantla, Nalini Vijay and Balmik, Abhishek Ankur and Dangi, Abha and Ramasamy, Sureshkumar and Marelli, Udaya Kiran and Chinnathambi, Subashchandrabose} } @article {46605, title = {HDAC6 ZnF UBP as the modifier of tau structure and function}, journal = {Biochemistry}, volume = {59}, year = {2020}, month = {DEC }, pages = {4546-4562}, type = {Article}, abstract = {

Histone deacetylase 6 is a class H histone deacetylase primarily present in the cytoplasm and involved in the regulation of various cellular functions. It consists of two catalytic deacetylase domains and a unique zinc finger ubiquitin binding protein domain, which sets it apart from other HDACs. HDAC6 is known to regulate cellular activities by modifying the function of microtubules, HSP90, and cortactin through deacetylation. Apart from the catalytic activity of HDAC6, it interacts with other proteins through either the SE14 domain or the ZnF UBP domain to modulate their functions. Here, we have studied the role of the HDAC6 ZnF UBP domain as a modifier of Tau aggregation by its direct interaction with the polyproline region/repeat region of Tau. Interaction of HDAC6 ZnF UBP with Tau was found to reduce the propensity of Tau to self-aggregate and to disaggregate preformed aggregates in a concentration-dependent manner and also bring about the conformational changes in Tau protein. The interaction of HDAC6 ZnF UBP with Tau results in its degradation, suggesting either proteolytic activity of HDAC6 ZnF UBP or its role in enhancing autoproteolysis of Tau.

}, issn = {0006-2960}, doi = {10.1021/acs.biochem.0c00585}, author = {Balmik, Abhishek Ankur and Chidambaram, Hariharakrishnan and Dangi, Abha and Marelli, Udaya Kiran and Chinnathambi, Subashchandrabose} } @article {46945, title = {Melatonin interacts with repeat domain of Tau to mediate disaggregation of paired helical filaments}, journal = {Biochimica Et Biophysica Acta-General Subjects}, volume = {1864}, year = {2020}, month = {MAR}, pages = {129467}, type = {Article}, abstract = {

Tau is the major neuronal protein involved in the stabilization of microtubule assembly. In Alzheimer{\textquoteright}s disease, Tau self-assembles to form intracellular protein aggregates which are toxic to cells. Various methods have been tried and tested to restrain the aggregation of Tau. Most of the agents tested for this purpose have limitations in their effectiveness and availability to neuronal cells. We have tested melatonin, a neurohormone secreted by pineal gland and a well-known anti-oxidant, for its ability to interact with the repeat domain of Tau using ITC and NMR. In aggregation inhibition and disaggregation studies of repeat Tau, melatonin was found to modulate the aggregation propensity of repeat Tau at a concentration of 5000 mu M and was more effective in dissolving preformed aggregates rather than acting as an aggregation inhibitor. However, there were no major conformational changes in Tau in presence of melatonin as observed by CD spectroscopy. On the basis of our findings, we are proposing a mechanism by which melatonin can interact with the repeat domain of Tau and exhibit its disaggregation effect.

}, keywords = {Alzheimer{\textquoteright}s disease, Disaggregation, melatonin, Paired helical filaments, tau protein, Tauopathies}, issn = {0304-4165}, doi = {10.1016/j.bbagen.2019.129467}, author = {Balmik, Abhishek Ankur and Das, Rashmi and Dangi, Abha and Gorantla, Nalini Vijay and Marelli, Udaya Kiran and Chinnathambi, Subashchandrabose} } @article {46894, title = {Novel cilengitide-based cyclic RGD peptides as alpha nu beta(3) integrin inhibitors}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {30}, year = {2020}, month = {APR}, pages = {127039}, type = {Article}, abstract = {

In this letter, we report a series of five new RGD-containing cyclic peptides as potent inhibitors to alpha nu beta(3) integrin protein. We have incorporated various unnatural lipophilic amino acids into the cyclic RGD framework of cilengitide, which is selective for alpha nu beta(3) integrin. All the newly synthesized cyclic peptides were evaluated in vitro solid phase binding assay and investigated for their binding behaviour towards integrin subtypes. All the cyclic peptides were synthesized in excellent yield following solution-phase coupling strategy. The cyclic RGD peptides 1a-e exhibited IC50 of 9.9, 5.5, 72, 11 and 3.3 nM, respectively, towards a alpha nu beta(3) integrin protein. This finding offers further opportunities for the introduction unusual amino acids into the cyclic peptide framework of cilengitide.

}, keywords = {Anticancer drugs, Cilengitide, Integrins, RGD cyclicpeptides}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2020.127039}, author = {Meena, Chhuttan L. and Singh, Dharmendra and Weinmueller, Michael and Reichart, Florian and Dangi, Abha and Marelli, Udaya Kiran and Zahler, Stefan and Sanjayan, Gangadhar J.} } @article {46773, title = {Residue-based propensity of aggregation in the Tau amyloidogenic hexapeptides AcPHF6*and AcPHF6}, journal = {RSC Advances}, volume = {10}, year = {2020}, month = {JUL}, pages = {27331-27335}, type = {Article}, abstract = {

In Alzheimer{\textquoteright}s disease and related tauopathies, the aggregation of microtubule-associated protein, Tau, into fibrils occursviathe interaction of two hexapeptide motifs PHF*(275)VQIINK(280)and PHF(306)VQIVYK(311)as beta-sheets. To understand the role of the constituent amino acids of PHF and PHF* in the aggregation, a set of 12 alanine mutant peptides was synthesized by replacing each amino acid in PHF and PHF* with alanine and they were characterized by nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), transmission electron microscopy (TEM) and ThS/ANS fluorescence assay. Our studies show that while the aggregation was suppressed in most of the alanine mutant peptides, replacement of glutamine by alanine in both PHF and PHF* enhanced the fibrillization.

}, doi = {10.1039/d0ra03809a}, author = {Dangi, Abha and Balmik, Abhishek Ankur and Ghorpade, Archana Kisan and Gorantla, Nalini Vijay and Sonawane, Shweta Kishor and Chinnathambi, Subashchandrabose and Marelli, Udaya Kiran} } @article {48936, title = {Exploration of N-arylation of backbone amides as a novel tool for conformational modification in peptides}, journal = {Chemistry- a european journal}, year = {2023}, month = {MAY}, type = {Journal Article}, abstract = {

A set of 15 cyclic-hexaalanine and 10 cyclic-pentaalanine peptides containing one or two backbone N-aryl amide bonds were synthesized by following a combination of solution-phase and solid-phase peptide synthesis. NMR-based conformation studies of these N-aryl cyclic-hexaalanine peptides revealed five distinct template conformations with an antiparallel beta-sheet structure; for N-aryl cyclic-pentaalanine peptides three template structures were revealed. All the template structures have distinct peptide-turn features. The conformations in these N-aryl peptides were compared to those in the commonly studied N-methyl peptide analogues. We observed that the N-aryl peptides exhibit a considerable conformational homogeneity, and their conformations differ significantly from those in N-methyl analogues. We anticipate that the N-arylation of backbone amides has the potential for application as a novel tool for conformation and physicochemical modification in peptides.

}, keywords = {cyclic peptides, N-arylation, N-modified amino acids, peptide conformation, peptide-based drug design}, issn = {0947-6539}, doi = {10.1002/chem.202300753}, author = {Dangi, Abha and Marelli, Udaya Kiran} } @article {48668, title = {Total synthesis, structure elucidation and expanded bioactivity of icosalide A: effect of lipophilicity and ester to amide substitution on its bioactivity}, journal = {Organic \& Biomolecular Chemistry}, volume = {21}, year = {2023}, month = {JUL}, pages = {5725-5731}, type = {Article}, abstract = {

The first total synthesis of icosalide A, an antibacterial depsipeptide that is unique in that it contains two lipophilic beta-hydroxy acids, has been achieved by following Fmoc solid-phase peptide synthesis in combination with solution-phase synthesis. The ambiguity in the absolute stereochemistry of icosalide A has been resolved by synthesizing the reported structures and other relevant diastereomers of icosalides and comparing their NMR data. NMR-based structure elucidation of icosalide A revealed a well-folded structure with cross-strand hydrogen bonds similar to the anti-parallel beta-sheet conformation in peptides and displayed a synergistic juxtaposition of the aliphatic sidechains. 12 analogues of icosalide A were synthesized by varying the constituent lipophilic beta-hydroxy acid residues, and their biological activities against Bacillus thuringiensis and Paenibacillus dendritiformis were explored. Most of these icosalide analogues showed an MIC of 12.5 \& mu;g mL(-1) against both bacteria. Swarming inhibition by icosalides was least in B. thuringiensis (8.3\%) compared to that in P. dendritiformis (33\%). Furthermore, this is the first report of icosalides showing assured inhibitory action (MIC between 2 and 10 \& mu;g mL(-1)) against the active stage of Mycobacterium tuberculosis and cancer cell lines such as HeLa and ThP1. This study could help optimize icosalides for anti-TB, antibacterial, and anti-cancer activities.

}, issn = {1477-0520}, doi = {10.1039/d3ob00809f}, author = {Dangi, Abha and Pande, Bharat and Agrawal, Sonia and Sarkar, Dhiman and Vamkudoth, Koteswara Rao and Marelli, Udaya Kiran} }