Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-XL: Role of Non-Hot Spot Residues

Background: Arteriovenous fistula (AVF) for hemodialysis integrates outward remodeling with vessel wall thickening in response to drastic hemodynamic changes. Aim of this study is to determine the role of Ki67, a well-established proliferative marker, related to AVF, and its relationship with time-dependent histological morphologic changes. Materials and methods: All patients were enrolled in 1 year and stratified in two groups: (A) pre-dialysis patients submitted to first AVF and (B) patients submitted to revision of AVF. Morphological changes: neo-angiogenesis (NAG), myointimal thickening (MIT), inflammatory infiltrate (IT), and aneurysmatic fistula degeneration (AD). The time of AVF creation was recorded. A biopsy of native vein in Group A and of arterialized vein in Group B was submitted to histological and immunohistochemical (IHC) analysis. IHC for Ki67 was automatically performed in all specimens. Ki67 immunoreactivity was assessed as the mean number of positive cells on several high-power fields, counted in the hot spots. Results: A total of 138 patients were enrolled, 69 (50.0%) Group A and 69 (50.0%) Group B. No NAG or MIT were found in Group A. Seven (10.1%) Group A veins showed a mild MIT. Analyzing the Group B, a moderate-to-severe MIT was present in 35 (50.7%), IT in 19 (27.5%), NAG in 37 (53.6%); AD was present in 10 (14.5%). All AVF of Group B with the exception of one (1.4%) showed a positivity for Ki67, with a mean of 12.31 ± 13.79 positive cells/hot spot (range 0–65). Ki67-immunoreactive cells had a subendothelial localization in 23 (33.3%) cases, a myointimal localization in SMC in 35 (50.7%) cases. The number of positive cells was significantly correlated with subendothelial localization of Ki67 ( p = 0.001) and with NA ( p = 0.001). Conclusions: Native veins do not contain cycling cells. In contrast, vascular cell proliferation starts immediately after AVF creation and persists independently of the time the fistula is set up. The amount of proliferating cells is significantly associated with MIT and subendothelial localization of Ki67-immunoreactive cells, thus suggesting a role of Ki-67 index in predicting AVF failure.

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Cortical Involvement in the Generation of Essential Tremor

Journal of Neurophysiology ◽

10.1152/jn.00477.2006 ◽

2007 ◽

Vol 97 (5) ◽

pp. 3219-3228 ◽

Cited By ~ 96

Author(s):

Jan Raethjen ◽

R. B. Govindan ◽

Florian Kopper ◽

M. Muthuraman ◽

Günther Deuschl

Keyword(s):

Essential Tremor ◽

Hot Spot ◽

Power Spectra ◽

Emg Activity ◽

Cortical Circuits ◽

Coherent Signals ◽

Cortical Motor ◽

Tremor Frequency ◽

Cortical Involvement

Conflicting results on the existence of tremor-related cortical activity in essential tremor (ET) have raised questions on the role of the cortex in tremor generation. Here we attempt to address these issues. We recorded 64 channel surface EEGs and EMGs from forearm muscles in 15 patients with definite ET. EEG and EMG power spectra, relative power of the rhythmic EMG activity, relative EEG power at the tremor frequency, and EEG–EMG and EEG–EEG coherence were calculated and their dynamics over time explored. Corticomuscular delay was studied using a new method for narrow-band coherent signals. Corticomuscular coherence in the contralateral central region at the tremor frequency was present in all patients in recordings with a relative tremor EMG power exceeding a certain level. However, the coherence was lost intermittently even with tremors far above this level. Physiological 15- to 30-Hz coherence was found consistently in 11 patients with significantly weaker EMG activity in this frequency range. A more frontal (mesial) hot spot was also intermittently coupled with the tremor and the central hot spot in five patients. Corticomuscular delays were compatible with transmission in fast corticospinal pathways and feedback of the tremor signal. Thus the tremor rhythm is intermittently relayed only in different cortical motor areas. We hypothesize that tremor oscillations build up in different subcortical and subcortico-cortical circuits only temporarily entraining each other.

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Macrocyclic Peptides as Allosteric Inhibitors of Nicotinamide N-Methyltransferase (NNMT)

10.26434/chemrxiv.12973130 ◽

2020 ◽

Author(s):

Matthijs J. van Haren ◽

Yurui Zhang ◽

Ned Buijs ◽

Vito Thijssen ◽

Davide Sartini ◽

...

Keyword(s):

Cyclic Peptides ◽

Cyclic Peptide ◽

Peptide Inhibitors ◽

Allosteric Inhibitors ◽

Disease States ◽

Potent Inhibition ◽

Macrocyclic Peptides ◽

Diabetes And Obesity ◽

Substrate Competition

Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide to form 1-methylnicotinamide using S-adenosyl-l-methionine (SAM) as the methyl donor. The complexity of the role of NNMT in healthy and disease states is slowly being elucidated and provides indication that NNMT may be an interesting therapeutic target for a variety of diseases including cancer, diabetes, and obesity. Most inhibitors of NNMT described to date are structurally related to one or both of its substrates. In search of structurally diverse NNMT inhibitors, an mRNA display screening technique was used to identify macrocyclic peptides which bind to NNMT. Several of the cyclic peptides identified in this manner show potent inhibition of NNMT with IC50 values as low as 229 nM. Interestingly, substrate competition experiments reveal that these cyclic peptide inhibitors are noncompetitive with either SAM or NA indicating they may be the first allosteric inhibitors reported for NNMT.

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Computational Design of Potent D-Peptide Inhibitors of SARS-CoV-2

Journal of Medicinal Chemistry ◽

10.1021/acs.jmedchem.1c00655 ◽

2021 ◽

Author(s):

Pedro A. Valiente ◽

Han Wen ◽

Satra Nim ◽

JinAh Lee ◽

Hyeon Ju Kim ◽

...

Keyword(s):

Computational Design ◽

Peptide Inhibitors

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Extending the Definition of the GyrB Quinolone Resistance-Determining Region in Mycobacterium tuberculosis DNA Gyrase for Assessing Fluoroquinolone Resistance in M. tuberculosis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.06272-11 ◽

2012 ◽

Vol 56 (4) ◽

pp. 1990-1996 ◽

Cited By ~ 40

Author(s):

Alix Pantel ◽

Stéphanie Petrella ◽

Nicolas Veziris ◽

Florence Brossier ◽

Sylvaine Bastian ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Hot Spot ◽

Dna Gyrase ◽

Quinolone Resistance ◽

Fluoroquinolone Resistance ◽

Wild Type ◽

Content Type ◽

Highly Active ◽

Definition Of

ABSTRACTFluoroquinolone (FQ) resistance is emerging inMycobacterium tuberculosis. The main mechanism of FQ resistance is amino acid substitution within the quinolone resistance-determining region (QRDR) of the GyrA subunit of DNA gyrase, the sole FQ target inM. tuberculosis. However, substitutions in GyrB whose implication in FQ resistance is unknown are increasingly being reported. The present study clarified the role of four GyrB substitutions identified inM. tuberculosisclinical strains, two located in the QRDR (D500A and N538T) and two outside the QRDR (T539P and E540V), in FQ resistance. We measured FQ MICs and also DNA gyrase inhibition by FQs in order to unequivocally clarify the role of these mutations in FQ resistance. Wild-type GyrA, wild-type GyrB, and mutant GyrB subunits produced from engineeredgyrBalleles by mutagenesis were overexpressed inEscherichia coli, purified to homogeneity, and used to reconstitute highly active gyrase complexes. MICs and DNA gyrase inhibition were determined for moxifloxacin, gatifloxacin, ofloxacin, levofloxacin, and enoxacin. All these substitutions are clearly implicated in FQ resistance, underlining the presence of a hot spot region housing most of the GyrB substitutions implicated in FQ resistance (residues NTE, 538 to 540). These findings help us to refine the definition of GyrB QRDR, which is extended to positions 500 to 540.

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Computational Design of Cyclic Peptide Inhibitors of the Anti-Apoptotic Protein Calbindin-D28K

Biochemistry & Pharmacology Open Access ◽

10.4172/2167-0501.1000142 ◽

2014 ◽

Vol 03 (04) ◽

Author(s):

Logan R Butler

Keyword(s):

Cyclic Peptide ◽

Computational Design ◽

Peptide Inhibitors ◽

Apoptotic Protein ◽

Calbindin D28k

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Hierarchy for targeting prosurvival BCL2 family proteins in multiple myeloma: pivotal role of MCL1

Blood ◽

10.1182/blood-2016-03-704908 ◽

2016 ◽

Vol 128 (14) ◽

pp. 1834-1844 ◽

Cited By ~ 78

Author(s):

Jia-Nan Gong ◽

Tiffany Khong ◽

David Segal ◽

Yuan Yao ◽

Chris D. Riffkin ◽

...

Keyword(s):

Multiple Myeloma ◽

Cell Lines ◽

Myeloma Cell ◽

Pivotal Role ◽

Bcl2 Family ◽

Key Points ◽

Low Passage ◽

Bh3 Mimetic

Key Points Only a minority of myeloma cell lines are killed when the prosurvival BCL2 or BCLXL are selectively inhibited with BH3 mimetic compounds. In contrast, targeting MCL1 readily killed ∼70% of the myeloma cell lines tested, including both low-passage and well-established ones.

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Lysine glutarylation in human sperm is associated with progressive motility

Human Reproduction ◽

10.1093/humrep/dez068 ◽

2019 ◽

Vol 34 (7) ◽

pp. 1186-1194 ◽

Cited By ~ 3

Author(s):

Yi-min Cheng ◽

Xiao-nian Hu ◽

Zhen Peng ◽

Ting-ting Pan ◽

Fang Wang ◽

...

Keyword(s):

Sperm Motility ◽

Natural Science ◽

Hot Spot ◽

Human Sperm ◽

Mature Sperm ◽

Computer Assisted ◽

Structured Illumination Microscopy ◽

Progressive Motility ◽

Wide Range

AbstractSTUDY QUESTIONIs there a role for lysine glutarylation (Kglu), a newly identified protein post-translational modification (PTM), in human sperm?SUMMARY ANSWERKglu occurs in several proteins located in the tail of human sperm, and it was reduced in asthenozoospermic (A) men and positively correlated with progressive motility of human sperm, indicating its important role in maintaining sperm motility.WHAT IS KNOWN ALREADYSince mature sperm are almost transcriptionally silent, PTM is regarded as an important pathway in regulating sperm function. However, only phosphorylation has been extensively studied in mature sperm to date. Protein lysine modification (PLM), a hot spot of PTMs, was rarely studied except for a few reports on lysine methylation and acetylation. As a newly identified PLM, Kglu has not been well characterized, especially in mature sperm.STUDY DESIGN, SIZE, DURATIONSperm samples were obtained from normozoospermic (N) men and A men who visited the reproductive medical center between February 2016 and January 2018. In total, 61 N men and 59 A men were recruited to participate in the study.PARTICIPANTS/MATERIALS, SETTING, METHODSKglu was examined by immunoblotting and immunofluorescence assays using a previously qualified pan-anti-glutaryllysine antibody that recognizes glutaryllysine in a wide range of sequence contexts (both in histones and non-histone substrates) but not the structurally similar malonyllysine and succinyllysine. The immunofluorescence assay was imaged using laser scanning confocal microscopy and super-resolution structured illumination microscopy. Sperm motility parameters were examined by computer-assisted sperm analysis.MAIN RESULTS AND THE ROLE OF CHANCEKglu occurs in several proteins (20–150 kDa) located in the tail of human sperm, especially in the middle piece and the latter part of the principal piece. Sperm Kglu was modulated by regulatory systems (enzymes and glutaryl-CoA) similar to those in HeLa cells. The mean level of sperm Kglu was significantly reduced in A men compared with N men (P < 0.001) and was positively correlated with progressive motility (P < 0.001). The sodium glutarate-induced elevation of Kglu levels in A men with lower Kglu levels in sperm significantly improved the progressive motility (P < 0.001). Furthermore, the reduced sperm Kglu levels in A men was accompanied by an increase in sperm glutaryl-CoA dehydrogenase (a regulatory enzyme of Kglu).LARGE SCALE DATAN/ALIMITATIONS, REASONS FOR CAUTIONAlthough the present study indicated the involvement of sperm Kglu in maintaining progressive motility of human sperm, the underlying mechanism needs to be investigated further.WIDER IMPLICATIONS OF THE FINDINGSThe findings of this study provide an insight into the novel role of Kglu in human sperm and suggest that abnormality of sperm PLMs may be one of the causes of asthenozoospermia.STUDY FUNDING/COMPETING INTEREST(S)National Natural Science Foundation of China (81 771 644 to T.L.; 31 671 204 to X.Z. and 81 871 207 to H.C.); National Basic Research Program of China (973 Program, 2015CB943003 to X.Z.); Natural Science Foundation of Jiangxi, China (20171ACB21006 and 20161BAB204167 to T.L.; 20165BCB18001 to X.Z.). The authors have no conflicts of interest to declare.

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