Facile synthesis of chiral N-, O and S-acyl isopeptides from tryptophan, tyrosine, and cysteine were done in single step for acquiring natural peptides via native chemical ligation (NCL). For the synthesis of chiral N-acyl isopeptides, tryptophane Cbz-(protected-α- aminoacyl)benzotriazoles were coupled with tryptophane to give Cbz-protected dipeptides. Further these dipeptides were N-acylated by Cbz-(protected-α-aminoacyl)benzotriazoles to obtain protected monoiso-tripeptides. In the synthesis of chiral O-acyl isopeptides from tyrosine Cbz-(protected-α-aminoacyl)benzotriazoles were coupled with tyrosine to give Cbzprotected dipeptides. And these dipeptides were O-acylated by Cbz-(protected-α- aminoacyl)benzotriazoles to synthesized protected monoiso-tripeptides. During the synthesis of chiral S-acyl isopeptides from cysteine Cbz-(protected-α-aminoacyl)benzotriazoles and dipeptidoyl benzotriazoles were coupled with cysteine to give Cbz-protected di and tripeptides. These cysteine containing di and tripeptides were S-acylated by Cbz-(protected- α-aminoacyl)benzotriazoles and dipeptidoyl benzotriazoles to prepare protected monoiso-tri- , tetra-, and penta-peptides. N-Acyl threonine isopeptides undergo acyl transfer in chemical ligations via 5-, 8-, 9- and 10-membered cyclic transition states to yield natural peptides, representing the first examples of successful isopeptide ligations from N-acyl threonine units. We synthesized the intermediate mono-isodipeptide to study the O-acyl migration from the oxygen to the Nterminal group of threonine amino acid sequence via a 5-membered transition state. However, it was also used as starting material to study the possibility of O- to N-acyl migration via 8-, 9- and 10-membered cyclic transition states. Mono-isodipeptide gave starting mono-isotripeptides on coupling with α-, β- or γ-amino acids for the ligation studies. To enhance migration rates, a glycine unit at the N-terminus of mono-isotripeptide - (((Benzyloxy)carbonyl)-L-alanyl)-N-((tert-butoxycarbonyl)glycyl)-L-threonine (122a) and β- and γ-amino acid units in mono-isotripeptides O-(((Benzyloxy)carbonyl)-L-alanyl)-N-(3- ((tert-butoxycarbonyl)amino)propanoyl)-L-threonine (122b) and O-(((Benzyloxy)carbonyl)- L-alanyl)-N-(4-((tert-butoxycarbonyl)amino)butanoyl)-L-threonine (122c) were used. Bocprotected mono-isodipeptide O-(((Benzyloxy)carbonyl)-L-alanyl)-N-(tert-butoxycarbonyl)- L-threonine (117) was obtained by the O-acylation of Boc-protected threonine with Cbz-LAla- Bt. Chemical ligation via a 5-membered cyclic transition state of unprotected monoisodipeptide O-(((Benzyloxy)carbonyl)-L-alanyl)-L-threonine hydrochloride (118) was investigated by using microwave irradiation in aqueous conditions (pH 7.3, 1 M buffer strength) as well as basic condition (DMF-piperidine). HPLC-MS (ESI) analysis of the ligated mixtures showed both in aqueous buffer as well as DMF-piperidine the expected migration product 5 (rt 38.08, m⁄z 325.0) together with intermolecular bis-acylation product 120 (rt 60.58, m⁄z 530.1). HPLC-HRMS, via (+) ESI-MS, confirmed that the ligated product 119 (rt 38.08, m⁄z 325.0) and starting mono-isohexapeptide 4 (rt 34.61, m⁄z 325.0) produced different MS patterns. Chemical ligation via a 8-, 9- and 10-membered cyclic transition state showed under aqueous conditions, (pH 7.3, 1 M buffer strength), 123a–c did not form the desired ligated products 124a–c or bis-acylated products 125a–c. Microwave irradiation of 123b in piperidine–DMF gave migration product 124b (57%) and intermolecular bisacylation product 125b (36%) as observed by HPLC-MS. We also observed bis-acylated product 125c in case of 123c. HPLC-MS, via (−)ESI-MS/MS, confirmed that 123b and 124b, had different fragmentation patterns, thus proving the formation of intramolecular ligated product 124b via a 9-membered TS. intramolecular acyl transfer through 5- and 9- membered transition states was favored over 8- and 11-membered transition state in basic condition. To synthesize quinolone and floroquinolone bis-conjugates, the carboxylic group of nalidixic acid and oxolinic acid were activated by using benzotriazole in presence of thionyl chloride. The Boc-protected aminoacylbenzotriazoles 129a–f were treated with ciprofloxacin 103 and norfloxacin 104 in the presence of triethylamine in DMF to obtain the conjugates 130a–f and 131a-f. The Boc-protected amino acid–antibiotic conjugates 130a–f and 131a-f were deprotected with a 1,4-dioxane–HCl mixture to give the unprotected amino acid–antibiotic conjugates 132a–f and 133a-f, which further were used in the next step without characterization. The target bis-conjugates 133a-f, 134a–f, 136a-f and 137a-f were prepared by coupling unprotected amino acid–antibiotic conjugates 132a–f and 135a-f with the benzotriazolide of nalidicxic acid 104 and oxolinic acid 105 in the presence of triethylamine in DMF. Few synthesized quinolones reveal mild antibacterial properties against Staphylococcus aureus (Gram positive bacteria) including 136a, 136d, and 137b (MIC = 32.9, 28.6and 30.6μM, respectively). Only compound 133f exhibits potent antibacterial properties against Staphylococcus aureus (MIC = 3.3 μM). These observations seem encouraging where, the starting precursors 101, 102, and 104 exhibit weak antibacterial properties (MIC = 3772.6, 3914.4, and 1345.6 μM, respectively) and 103 views mild properties (MIC = 74.4 μM) against Staphylococcus aureus. Additionally, only compound 133b among all the tested quinolones, exhibits promising antibacterial properties (MIC = 7.8 μM) against Streptococcus pyogenes (Gram positive bacteria) considering that, the starting precursors 101, 102, 103,and 104 reveal weak antibacterial properties (MIC = 3772.6, 1957.2, 2383.5, and 1345.6 μM, respectively) against this tested microorganism. On the other hand, most of the starting quinolone antibiotics (101, 102, 103, and 104) used in the present study reveal potent properties (MIC = 7.2, 7.5, 9.2, and 10.3 μM, respectively) against Salmonella Typhi (Gram negative bacteria). Synthesized quinolones 134a, and 134b reveal promising potency (MIC = 7.6, and 7.4 μM, respectively). Other synthesized analogues (133b, and 134f) exhibit mild antibacterial properties (MIC = 15.7, and 25.5 μM, respectively) against Salmonella Typhi. It has also been noticed that, none of the synthesized quinolones reveal either potent or mild properties against Pseudomonas aeruginosa (Gram negative bacteria, MIC ≥ 409.2 μM) considering that the starting quinolines 101, and 102 used in the present study reveal mild properties (MIC = 14.5, and 15.0 μM, respectively), but 103, and 104 view weak antibacterial properties (MIC = 74.4, and 336.3 μM, respectively). The QSAR model predicted MIC values due to all the potent antibacterial active agents against Salmonella Typhi are close to the experimental ones suggesting that the model is statistically significant (e.g. compounds 101, 102, 103, 104, 134a, and 134b, with observed MIC values = 7.2, 7.5, 9.2, 10.3, 7.6, and 7.4 μM; predicted MIC values = 7.0, 8.6, 7.6, 11.9, 11.6, and 9.8 μM; giving error values = 0.2, -1.1, 1.6, -1.6, -4.0, and -2.4, respectively). The same appears to be the case for the compounds exhibiting mild antibacterial potency (e.g. compound 133b, with observed MIC value = 15.7μM, against predicted value = 14.9 μM, error value = 0.8). Moreover, all the weak antibacterial active agents reveal high error values due to high difference between the observed and predicted MIC’s explaining that the attained QSAR model is applicable only to the highly potent and mild antibacterial agents against Salmonella Typhi, suggesting that the QSAR model has a good predictive capacity.